Data Intake
| Index | stub | file | data_type | taxon_string | translation_table |
|---|---|---|---|---|---|
| 0 | KX808498-truncated | KX808498-truncated.gb | GenBank | Caulerpa_cliftonii_HV03798 | 11 |
| 1 | KY509313-truncated | KY509313-truncated.gb | GenBank | Avrainvillea_mazei_HV02664 | 11 |
| 2 | MH591083-truncated | MH591083-truncated.gb | GenBank | Flabellia_petiolata_HV01202 | 11 |
| 3 | MH591084-truncated | MH591084-truncated.gb | GenBank | Flabellia_petiolata_HV01202 | 11 |
| 4 | MH591085-truncated | MH591085-truncated.gb | GenBank | Flabellia_petiolata_HV01202 | 11 |
| 5 | NC_026795-truncated | NC_026795-truncated.txt | GenBank | Bryopsis_plumosa_WEST4718 | 11 |
| 6 | KY819064-truncated-cds | KY819064-truncated.cds.fasta | CDS | Chlorodesmis_fastigiata_HV03865 | 11 |
| 7 | KX808497-truncated | KX808497-truncated.fa | CDS | Derbesia_sp_WEST4838 | 11 |
Orthofinder
| Orthogroup | KX808497-truncated.translated | KX808498-truncated.translated | KY509313-truncated.translated | KY819064-truncated-cds.translated | MH591083-truncated.translated | MH591084-truncated.translated | MH591085-truncated.translated | NC_026795-truncated.translated |
|---|---|---|---|---|---|---|---|---|
| OG0000000 | Derbesia_sp_WEST4838|KX808497-truncated.fa|0|KX808497.1|petA | Caulerpa_cliftonii_HV03798|KX808498-truncated.gb|23|petA | Avrainvillea_mazei_HV02664|KY509313-truncated.gb|0|petA | Chlorodesmis_fastigiata_HV03865|KY819064-truncated.cds.fasta|0|KY819064.1|petA | — | Flabellia_petiolata_HV01202|MH591084-truncated.gb|0|petA | — | Bryopsis_plumosa_WEST4718|NC_026795-truncated.txt|0|petA |
| OG0000001 | Derbesia_sp_WEST4838|KX808497-truncated.fa|1|KX808497.1|rpl23 | Caulerpa_cliftonii_HV03798|KX808498-truncated.gb|22|rpl23 | Avrainvillea_mazei_HV02664|KY509313-truncated.gb|3|rpl23 | Chlorodesmis_fastigiata_HV03865|KY819064-truncated.cds.fasta|1|KY819064.1|rpl23 | — | Flabellia_petiolata_HV01202|MH591084-truncated.gb|1|rpl23 | — | Bryopsis_plumosa_WEST4718|NC_026795-truncated.txt|1|rpl23 |
| OG0000002 | Derbesia_sp_WEST4838|KX808497-truncated.fa|2|KX808497.1|psaI | Caulerpa_cliftonii_HV03798|KX808498-truncated.gb|24|psaI | Avrainvillea_mazei_HV02664|KY509313-truncated.gb|1|psaI | Chlorodesmis_fastigiata_HV03865|KY819064-truncated.cds.fasta|2|KY819064.1|psaI | Flabellia_petiolata_HV01202|MH591083-truncated.gb|1|psaI | — | — | Bryopsis_plumosa_WEST4718|NC_026795-truncated.txt|2|psaI |
| OG0000003 | Derbesia_sp_WEST4838|KX808497-truncated.fa|3|KX808497.1|petG | Caulerpa_cliftonii_HV03798|KX808498-truncated.gb|26|petG | Avrainvillea_mazei_HV02664|KY509313-truncated.gb|2|petG | Chlorodesmis_fastigiata_HV03865|KY819064-truncated.cds.fasta|3|KY819064.1|petG | Flabellia_petiolata_HV01202|MH591083-truncated.gb|0|petG | — | — | Bryopsis_plumosa_WEST4718|NC_026795-truncated.txt|3|petG |
| OG0000004 | Derbesia_sp_WEST4838|KX808497-truncated.fa|4|KX808497.1|rbcL | Caulerpa_cliftonii_HV03798|KX808498-truncated.gb|27|rbcL | Avrainvillea_mazei_HV02664|KY509313-truncated.gb|4|rbcL | Chlorodesmis_fastigiata_HV03865|KY819064-truncated.cds.fasta|4|KY819064.1|rbcL | Flabellia_petiolata_HV01202|MH591083-truncated.gb|2|rbcL | — | — | Bryopsis_plumosa_WEST4718|NC_026795-truncated.txt|4|rbcL |
| OG0000005 | Derbesia_sp_WEST4838|KX808497-truncated.fa|6|KX808497.1|rps18 | Caulerpa_cliftonii_HV03798|KX808498-truncated.gb|29|rps18, Caulerpa_cliftonii_HV03798|KX808498-truncated.gb|30|orf179 | Avrainvillea_mazei_HV02664|KY509313-truncated.gb|5|rps18 | Chlorodesmis_fastigiata_HV03865|KY819064-truncated.cds.fasta|6|KY819064.1|rps18 | — | — | — | Bryopsis_plumosa_WEST4718|NC_026795-truncated.txt|6|rps18 |
| OG0000006 | Derbesia_sp_WEST4838|KX808497-truncated.fa|5|KX808497.1|psbE | Caulerpa_cliftonii_HV03798|KX808498-truncated.gb|28|psbE | Avrainvillea_mazei_HV02664|KY509313-truncated.gb|6|psbE | Chlorodesmis_fastigiata_HV03865|KY819064-truncated.cds.fasta|5|KY819064.1|psbE | — | — | — | Bryopsis_plumosa_WEST4718|NC_026795-truncated.txt|5|psbE |
| Orthogroup | KX808497-truncated.translated | KX808498-truncated.translated | KY509313-truncated.translated | KY819064-truncated-cds.translated | MH591083-truncated.translated | MH591084-truncated.translated | MH591085-truncated.translated | NC_026795-truncated.translated |
|---|---|---|---|---|---|---|---|---|
| OG0000007 | — | Caulerpa_cliftonii_HV03798|KX808498-truncated.gb|0|rps9 | — | — | — | — | — | — |
| OG0000008 | — | Caulerpa_cliftonii_HV03798|KX808498-truncated.gb|1|rpoC1 | — | — | — | — | — | — |
| OG0000009 | — | Caulerpa_cliftonii_HV03798|KX808498-truncated.gb|2|rpoC2 | — | — | — | — | — | — |
| OG0000010 | — | Caulerpa_cliftonii_HV03798|KX808498-truncated.gb|3|psaB | — | — | — | — | — | — |
| OG0000011 | — | Caulerpa_cliftonii_HV03798|KX808498-truncated.gb|4|psbZ | — | — | — | — | — | — |
| OG0000012 | — | Caulerpa_cliftonii_HV03798|KX808498-truncated.gb|5|orf180 | — | — | — | — | — | — |
| OG0000013 | — | Caulerpa_cliftonii_HV03798|KX808498-truncated.gb|6|orf116 | — | — | — | — | — | — |
| OG0000014 | — | Caulerpa_cliftonii_HV03798|KX808498-truncated.gb|7|orf144 | — | — | — | — | — | — |
| OG0000015 | — | Caulerpa_cliftonii_HV03798|KX808498-truncated.gb|8|orf519 | — | — | — | — | — | — |
| OG0000016 | — | Caulerpa_cliftonii_HV03798|KX808498-truncated.gb|9|psbA | — | — | — | — | — | — |
| OG0000017 | — | Caulerpa_cliftonii_HV03798|KX808498-truncated.gb|10|orf128 | — | — | — | — | — | — |
| OG0000018 | — | Caulerpa_cliftonii_HV03798|KX808498-truncated.gb|11|rpoA | — | — | — | — | — | — |
| OG0000019 | — | Caulerpa_cliftonii_HV03798|KX808498-truncated.gb|12|rps11 | — | — | — | — | — | — |
| OG0000020 | — | Caulerpa_cliftonii_HV03798|KX808498-truncated.gb|13|rpl36 | — | — | — | — | — | — |
| OG0000021 | — | Caulerpa_cliftonii_HV03798|KX808498-truncated.gb|14|infA | — | — | — | — | — | — |
| OG0000022 | — | Caulerpa_cliftonii_HV03798|KX808498-truncated.gb|15|rps8 | — | — | — | — | — | — |
| OG0000023 | — | Caulerpa_cliftonii_HV03798|KX808498-truncated.gb|16|rpl5 | — | — | — | — | — | — |
| OG0000024 | — | Caulerpa_cliftonii_HV03798|KX808498-truncated.gb|17|rpl14 | — | — | — | — | — | — |
| OG0000025 | — | Caulerpa_cliftonii_HV03798|KX808498-truncated.gb|18|rpl16 | — | — | — | — | — | — |
| OG0000026 | — | Caulerpa_cliftonii_HV03798|KX808498-truncated.gb|19|rps3 | — | — | — | — | — | — |
| OG0000027 | — | Caulerpa_cliftonii_HV03798|KX808498-truncated.gb|20|rps19 | — | — | — | — | — | — |
| OG0000028 | — | Caulerpa_cliftonii_HV03798|KX808498-truncated.gb|21|rpl2 | — | — | — | — | — | — |
| OG0000029 | — | Caulerpa_cliftonii_HV03798|KX808498-truncated.gb|25|ycf20 | — | — | — | — | — | — |
| OG0000030 | — | — | — | — | — | — | Flabellia_petiolata_HV01202|MH591085-truncated.gb|0|psbE | — |
| Input | KX808497-truncated.translated | KX808498-truncated.translated | KY509313-truncated.translated | KY819064-truncated-cds.translated | MH591083-truncated.translated | MH591084-truncated.translated | MH591085-truncated.translated | NC_026795-truncated.translated |
|---|---|---|---|---|---|---|---|---|
| KX808497-truncated.translated | 7 | 7 | 7 | 7 | 3 | 2 | 0 | 7 |
| KX808498-truncated.translated | 7 | 7 | 7 | 7 | 3 | 2 | 0 | 7 |
| KY509313-truncated.translated | 7 | 7 | 7 | 7 | 3 | 2 | 0 | 7 |
| KY819064-truncated-cds.translated | 7 | 7 | 7 | 7 | 3 | 2 | 0 | 7 |
| MH591083-truncated.translated | 3 | 3 | 3 | 3 | 3 | 0 | 0 | 3 |
| MH591084-truncated.translated | 2 | 2 | 2 | 2 | 0 | 2 | 0 | 2 |
| MH591085-truncated.translated | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 |
| NC_026795-truncated.translated | 7 | 7 | 7 | 7 | 3 | 2 | 0 | 7 |
results/orthofinder/output/Orthogroup_Sequences/OG0000000.fa results/orthofinder/output/Orthogroup_Sequences/OG0000001.fa results/orthofinder/output/Orthogroup_Sequences/OG0000002.fa results/orthofinder/output/Orthogroup_Sequences/OG0000003.fa results/orthofinder/output/Orthogroup_Sequences/OG0000004.fa results/orthofinder/output/Orthogroup_Sequences/OG0000006.fa
results/orthofinder/orthosnap/OG0000005/OG0000005_orthosnap_0.fa
Alignment
results/alignment/trimmed_cds/OG0000004.trimmed.cds.alignment.fa results/alignment/trimmed_cds/OG0000000.trimmed.cds.alignment.fa
Supermatrix
General Characteristics ======================= 6 Number of taxa 2388 Alignment length 496 Parsimony informative sites 496 Variable sites 1882 Constant sites Character Frequencies ===================== T 4524 G 2766 C 2251 A 4643 - 144
IQ-TREE 2.2.0.3 COVID-edition built Aug 2 2022
Input file name: results/supermatrix/supermatrix.cds.fa
Type of analysis: ModelFinder + tree reconstruction + ultrafast bootstrap (1000 replicates)
Random seed number: 161615
REFERENCES
----------
To cite IQ-TREE please use:
Bui Quang Minh, Heiko A. Schmidt, Olga Chernomor, Dominik Schrempf,
Michael D. Woodhams, Arndt von Haeseler, and Robert Lanfear (2020)
IQ-TREE 2: New models and efficient methods for phylogenetic inference
in the genomic era. Mol. Biol. Evol., in press.
https://doi.org/10.1093/molbev/msaa015
To cite ModelFinder please use:
Subha Kalyaanamoorthy, Bui Quang Minh, Thomas KF Wong, Arndt von Haeseler,
and Lars S Jermiin (2017) ModelFinder: Fast model selection for
accurate phylogenetic estimates. Nature Methods, 14:587–589.
https://doi.org/10.1038/nmeth.4285
Since you used ultrafast bootstrap (UFBoot) please also cite:
Diep Thi Hoang, Olga Chernomor, Arndt von Haeseler, Bui Quang Minh,
and Le Sy Vinh (2018) UFBoot2: Improving the ultrafast bootstrap
approximation. Mol. Biol. Evol., 35:518–522.
https://doi.org/10.1093/molbev/msx281
SEQUENCE ALIGNMENT
------------------
Input data: 6 sequences with 2388 nucleotide sites
Number of constant sites: 1400 (= 58.6265% of all sites)
Number of invariant (constant or ambiguous constant) sites: 1400 (= 58.6265% of all sites)
Number of parsimony informative sites: 496
Number of distinct site patterns: 492
ModelFinder
-----------
Best-fit model according to BIC: GTR+F+G4
List of models sorted by BIC scores:
Model LogL AIC w-AIC AICc w-AICc BIC w-BIC
GTR+F+G4 -9950.622 19937.245 + 0.254 19937.534 + 0.257 20041.253 + 0.464
TIM2+F+G4 -9958.889 19949.778 - 0.000483 19950.007 - 0.000503 20042.229 + 0.285
TIM2+F+I -9960.089 19952.178 - 0.000145 19952.407 - 0.000152 20044.629 + 0.0857
GTR+F+I+G4 -9948.579 19935.159 + 0.721 19935.480 + 0.718 20044.945 + 0.0732
TIM2+F+I+G4 -9956.690 19947.381 - 0.0016 19947.639 - 0.00164 20045.610 + 0.0525
GTR+F+I -9953.065 19942.130 - 0.0221 19942.419 - 0.0224 20046.138 - 0.0403
TPM2u+F+I -9976.669 19983.337 - 2.49e-11 19983.540 - 2.63e-11 20070.011 - 2.64e-07
TVM+F+I -9969.542 19973.084 - 4.2e-09 19973.343 - 4.31e-09 20071.314 - 1.38e-07
TVM+F+G4 -9970.077 19974.155 - 2.46e-09 19974.413 - 2.52e-09 20072.384 - 8.05e-08
TPM2u+F+G4 -9978.794 19987.588 - 2.97e-12 19987.790 - 3.14e-12 20074.261 - 3.15e-08
TVM+F+I+G4 -9968.124 19972.249 - 6.37e-09 19972.537 - 6.45e-09 20076.256 - 1.16e-08
TIM+F+G4 -9976.342 19984.683 - 1.27e-11 19984.913 - 1.32e-11 20077.135 - 7.49e-09
TPM2u+F+I+G4 -9976.786 19985.571 - 8.15e-12 19985.801 - 8.49e-12 20078.023 - 4.81e-09
TIM+F+I -9978.268 19988.535 - 1.85e-12 19988.765 - 1.93e-12 20080.987 - 1.09e-09
TIM+F+I+G4 -9974.947 19983.894 - 1.89e-11 19984.152 - 1.94e-11 20082.123 - 6.18e-10
K3Pu+F+I -9994.574 20019.149 - 4.17e-19 20019.351 - 4.4e-19 20105.822 - 4.42e-15
K3Pu+F+G4 -9997.747 20025.495 - 1.75e-20 20025.697 - 1.84e-20 20112.168 - 1.85e-16
K3Pu+F+I+G4 -9996.293 20024.586 - 2.75e-20 20024.816 - 2.87e-20 20117.038 - 1.62e-17
TN+F+G4 -10003.782 20037.564 - 4.18e-23 20037.767 - 4.41e-23 20124.237 - 4.43e-19
TN+F+I -10005.761 20041.522 - 5.78e-24 20041.724 - 6.1e-24 20128.195 - 6.12e-20
TN+F+I+G4 -10002.313 20036.626 - 6.68e-23 20036.856 - 6.96e-23 20129.078 - 3.94e-20
TIM3+F+G4 -10003.134 20038.269 - 2.94e-23 20038.498 - 3.06e-23 20130.720 - 1.73e-20
TIM3+F+I -10004.794 20041.588 - 5.59e-24 20041.817 - 5.83e-24 20134.039 - 3.3e-21
TIM3+F+I+G4 -10001.831 20037.662 - 3.98e-23 20037.920 - 4.09e-23 20135.892 - 1.31e-21
HKY+F+I -10020.421 20068.842 - 6.75e-30 20069.019 - 7.22e-30 20149.737 - 1.29e-24
TPM3u+F+I -10019.385 20068.770 - 7e-30 20068.972 - 7.39e-30 20155.443 - 7.41e-26
HKY+F+G4 -10023.678 20075.356 - 2.6e-31 20075.533 - 2.78e-31 20156.251 - 4.95e-26
HKY+F+I+G4 -10022.196 20074.393 - 4.21e-31 20074.595 - 4.44e-31 20161.066 - 4.46e-27
TPM3u+F+G4 -10022.668 20075.336 - 2.63e-31 20075.538 - 2.77e-31 20162.009 - 2.78e-27
TPM3u+F+I+G4 -10021.313 20074.626 - 3.74e-31 20074.855 - 3.9e-31 20167.077 - 2.21e-28
F81+F+I -10041.407 20108.815 - 1.41e-38 20108.968 - 1.53e-38 20183.932 - 4.83e-32
F81+F+G4 -10046.374 20118.748 - 9.82e-41 20118.901 - 1.06e-40 20193.865 - 3.36e-34
F81+F+I+G4 -10044.860 20117.720 - 1.64e-40 20117.897 - 1.76e-40 20198.615 - 3.13e-35
SYM+I -10106.619 20243.238 - 9.11e-68 20243.440 - 9.62e-68 20329.911 - 9.66e-64
TVMe+I -10112.050 20252.100 - 1.08e-69 20252.277 - 1.16e-69 20332.995 - 2.07e-64
SYM+G4 -10109.264 20248.529 - 6.47e-69 20248.731 - 6.83e-69 20335.202 - 6.85e-65
SYM+I+G4 -10105.978 20243.957 - 6.36e-68 20244.186 - 6.63e-68 20336.408 - 3.75e-65
TVMe+G4 -10115.760 20259.521 - 2.65e-71 20259.698 - 2.84e-71 20340.416 - 5.06e-66
TVMe+I+G4 -10112.239 20254.478 - 3.3e-70 20254.680 - 3.49e-70 20341.151 - 3.5e-66
TIM2e+I -10159.736 20345.473 - 5.75e-90 20345.626 - 6.22e-90 20420.589 - 1.97e-83
TPM2+I -10164.413 20352.827 - 1.45e-91 20352.958 - 1.59e-91 20422.165 - 8.96e-84
TIM2e+I+G4 -10162.604 20353.209 - 1.2e-91 20353.386 - 1.29e-91 20434.104 - 2.29e-86
TIM2e+G4 -10166.496 20358.992 - 6.67e-93 20359.145 - 7.22e-93 20434.109 - 2.28e-86
TPM2+I+G4 -10167.174 20360.347 - 3.39e-93 20360.500 - 3.67e-93 20435.464 - 1.16e-86
TPM2+G4 -10171.100 20366.199 - 1.82e-94 20366.330 - 1.99e-94 20435.538 - 1.12e-86
TIMe+I -10187.704 20401.408 - 4.11e-102 20401.562 - 4.44e-102 20476.525 - 1.41e-95
K3P+I -10193.175 20410.349 - 4.7e-104 20410.480 - 5.14e-104 20479.688 - 2.89e-96
TIMe+G4 -10195.091 20416.182 - 2.54e-105 20416.335 - 2.75e-105 20491.298 - 8.71e-99
TIMe+I+G4 -10192.910 20413.821 - 8.28e-105 20413.998 - 8.86e-105 20494.716 - 1.58e-99
K3P+G4 -10203.234 20430.468 - 2.01e-108 20430.600 - 2.2e-108 20499.807 - 1.24e-100
K3P+I+G4 -10200.723 20427.446 - 9.11e-108 20427.600 - 9.86e-108 20502.563 - 3.12e-101
TIM3e+I -10233.779 20493.557 - 4.01e-122 20493.711 - 4.34e-122 20568.674 - 1.37e-115
TIM3e+G4 -10234.984 20495.968 - 1.2e-122 20496.121 - 1.3e-122 20571.085 - 4.12e-116
TPM3+I -10240.588 20505.176 - 1.2e-124 20505.307 - 1.32e-124 20574.515 - 7.41e-117
TIM3e+I+G4 -10233.164 20494.327 - 2.73e-122 20494.504 - 2.92e-122 20575.222 - 5.2e-117
TPM3+G4 -10246.096 20516.192 - 4.88e-127 20516.324 - 5.34e-127 20585.531 - 3e-119
TPM3+I+G4 -10243.636 20513.272 - 2.1e-126 20513.425 - 2.27e-126 20588.389 - 7.2e-120
GTR+F -10231.559 20497.118 - 6.77e-123 20497.376 - 6.95e-123 20595.348 - 2.22e-121
TNe+I -10266.205 20556.409 - 9.02e-136 20556.541 - 9.87e-136 20625.748 - 5.56e-128
JC+I -10275.298 20570.596 - 7.49e-139 20570.689 - 8.36e-139 20628.378 - 1.49e-128
K2P+I -10272.035 20566.071 - 7.2e-138 20566.182 - 7.96e-138 20629.631 - 7.97e-129
TNe+G4 -10273.280 20570.561 - 7.63e-139 20570.692 - 8.35e-139 20639.899 - 4.7e-131
TNe+I+G4 -10271.035 20568.070 - 2.65e-138 20568.223 - 2.87e-138 20643.186 - 9.08e-132
K2P+G4 -10281.744 20585.488 - 4.37e-142 20585.599 - 4.84e-142 20649.049 - 4.84e-133
JC+G4 -10285.852 20591.704 - 1.96e-143 20591.796 - 2.18e-143 20649.486 - 3.89e-133
K2P+I+G4 -10279.249 20582.498 - 1.95e-141 20582.630 - 2.14e-141 20651.837 - 1.2e-133
JC+I+G4 -10283.324 20588.649 - 9.01e-143 20588.760 - 9.96e-143 20652.209 - 9.97e-134
AIC, w-AIC : Akaike information criterion scores and weights.
AICc, w-AICc : Corrected AIC scores and weights.
BIC, w-BIC : Bayesian information criterion scores and weights.
Plus signs denote the 95% confidence sets.
Minus signs denote significant exclusion.
SUBSTITUTION PROCESS
--------------------
Model of substitution: GTR+F+G4
Rate parameter R:
A-C: 2.6505
A-G: 2.9500
A-T: 3.9453
C-G: 1.9541
C-T: 6.1752
G-T: 1.0000
State frequencies: (empirical counts from alignment)
pi(A) = 0.3273
pi(C) = 0.1587
pi(G) = 0.195
pi(T) = 0.319
Rate matrix Q:
A -0.9608 0.1793 0.2452 0.5363
C 0.3698 -1.372 0.1624 0.8394
G 0.4116 0.1322 -0.6797 0.1359
T 0.5504 0.4177 0.08311 -1.051
Model of rate heterogeneity: Gamma with 4 categories
Gamma shape alpha: 0.3949
Category Relative_rate Proportion
1 0.01598 0.25
2 0.1779 0.25
3 0.7257 0.25
4 3.08 0.25
Relative rates are computed as MEAN of the portion of the Gamma distribution falling in the category.
MAXIMUM LIKELIHOOD TREE
-----------------------
Log-likelihood of the tree: -9950.6201 (s.e. 142.9199)
Unconstrained log-likelihood (without tree): -9284.4483
Number of free parameters (#branches + #model parameters): 18
Akaike information criterion (AIC) score: 19937.2401
Corrected Akaike information criterion (AICc) score: 19937.5288
Bayesian information criterion (BIC) score: 20041.2479
Total tree length (sum of branch lengths): 1.0856
Sum of internal branch lengths: 0.2051 (18.8890% of tree length)
NOTE: Tree is UNROOTED although outgroup taxon 'Avrainvillea_mazei_HV02664' is drawn at root
Numbers in parentheses are ultrafast bootstrap support (%)
+-----------------------------------------------Avrainvillea_mazei_HV02664
|
| +--------------------------------Bryopsis_plumosa_WEST4718
+----------------| (100)
| +-----------------------------------------Derbesia_sp_WEST4838
|
| +--------------------------------------Caulerpa_cliftonii_HV03798
+------------------| (100)
| +---------------------Chlorodesmis_fastigiata_HV03865
+---------| (98)
+----------------Flabellia_petiolata_HV01202
Tree in newick format:
(Avrainvillea_mazei_HV02664:0.2083416424,(Bryopsis_plumosa_WEST4718:0.1431662975,Derbesia_sp_WEST4838:0.1843593970)100:0.0749149176,(Caulerpa_cliftonii_HV03798:0.1700810002,(Chlorodesmis_fastigiata_HV03865:0.0968424550,Flabellia_petiolata_HV01202:0.0777150973)98:0.0437233286)100:0.0864127563);
CONSENSUS TREE
--------------
Consensus tree is constructed from 1000 bootstrap trees
Log-likelihood of consensus tree: -9950.620052
Robinson-Foulds distance between ML tree and consensus tree: 0
Branches with support >0.000000% are kept (extended consensus)
Branch lengths are optimized by maximum likelihood on original alignment
Numbers in parentheses are bootstrap supports (%)
+-----------------------------------------------Avrainvillea_mazei_HV02664
|
| +--------------------------------Bryopsis_plumosa_WEST4718
+----------------| (100)
| +-----------------------------------------Derbesia_sp_WEST4838
|
| +--------------------------------------Caulerpa_cliftonii_HV03798
+------------------| (100)
| +---------------------Chlorodesmis_fastigiata_HV03865
+---------| (98)
+----------------Flabellia_petiolata_HV01202
Consensus tree in newick format:
(Avrainvillea_mazei_HV02664:0.2083451933,(Bryopsis_plumosa_WEST4718:0.1431632302,Derbesia_sp_WEST4838:0.1843631097)100:0.0749217475,(Caulerpa_cliftonii_HV03798:0.1701007202,(Chlorodesmis_fastigiata_HV03865:0.0968536522,Flabellia_petiolata_HV01202:0.0777184217)98:0.0437063646)100:0.0864044165);
TIME STAMP
----------
Date and time: Sat Dec 16 03:48:38 2023
Total CPU time used: 3534.348888 seconds (0h:58m:54s)
Total wall-clock time used: 138.9548088 seconds (0h:2m:18s)
IQ-TREE multicore version 2.2.0.3 COVID-edition for Linux 64-bit built Aug 2 2022
Developed by Bui Quang Minh, James Barbetti, Nguyen Lam Tung,
Olga Chernomor, Heiko Schmidt, Dominik Schrempf, Michael Woodhams, Ly Trong Nhan.
Host: herbairumphylo (AVX512, FMA3, 283 GB RAM)
Command: iqtree2 -s results/supermatrix/supermatrix.cds.fa -bb 1000 -m TEST -nt 32 -redo
Seed: 161615 (Using SPRNG - Scalable Parallel Random Number Generator)
Time: Sat Dec 16 03:42:46 2023
Kernel: AVX+FMA - 32 threads (32 CPU cores detected)
Reading alignment file results/supermatrix/supermatrix.cds.fa ... Fasta format detected
Reading fasta file: done in 0.000622578 secs
Alignment most likely contains DNA/RNA sequences
Constructing alignment: done in 0.00448822 secs using 867.2% CPU
Alignment has 6 sequences with 2388 columns, 492 distinct patterns
496 parsimony-informative, 492 singleton sites, 1399 constant sites
Gap/Ambiguity Composition p-value
Analyzing sequences: done in 0.020126 secs using 579.1% CPU
1 Avrainvillea_mazei_HV02664 1.13% passed 34.31%
2 Bryopsis_plumosa_WEST4718 0.38% passed 73.08%
3 Caulerpa_cliftonii_HV03798 0.00% passed 67.19%
4 Chlorodesmis_fastigiata_HV03865 1.51% passed 91.03%
5 Derbesia_sp_WEST4838 0.63% passed 90.09%
6 Flabellia_petiolata_HV01202 2.39% passed 90.54%
**** TOTAL 1.01% 0 sequences failed composition chi2 test (p-value<5%; df=3)
Checking for duplicate sequences: done in 0.0198425 secs using 584.8% CPU
Create initial parsimony tree by phylogenetic likelihood library (PLL)... 0.004 seconds
WARNING: Number of threads seems too high for short alignments. Use -T AUTO to determine best number of threads.
Perform fast likelihood tree search using GTR+I+G model...
Estimate model parameters (epsilon = 5.000)
Perform nearest neighbor interchange...
Optimizing NNI: done in 1.81597 secs using 816.4% CPU
Estimate model parameters (epsilon = 1.000)
1. Initial log-likelihood: -9948.592
Optimal log-likelihood: -9948.559
Rate parameters: A-C: 2.77621 A-G: 3.02265 A-T: 4.05715 C-G: 2.02910 C-T: 6.35200 G-T: 1.00000
Base frequencies: A: 0.327 C: 0.159 G: 0.195 T: 0.319
Proportion of invariable sites: 0.294
Gamma shape alpha: 0.898
Parameters optimization took 1 rounds (1.082 sec)
Time for fast ML tree search: 11.582 seconds
NOTE: ModelFinder requires 2 MB RAM!
ModelFinder will test up to 88 DNA models (sample size: 2388) ...
No. Model -LnL df AIC AICc BIC
WARNING: Number of threads seems too high for short alignments. Use -T AUTO to determine best number of threads.
1 GTR+F 10231.559 17 20497.118 20497.376 20595.348
WARNING: Number of threads seems too high for short alignments. Use -T AUTO to determine best number of threads.
2 GTR+F+I 9953.065 18 19942.130 19942.419 20046.138
WARNING: Number of threads seems too high for short alignments. Use -T AUTO to determine best number of threads.
3 GTR+F+G4 9950.622 18 19937.245 19937.534 20041.253
WARNING: Number of threads seems too high for short alignments. Use -T AUTO to determine best number of threads.
4 GTR+F+I+G4 9948.579 19 19935.159 19935.480 20044.945
WARNING: Number of threads seems too high for short alignments. Use -T AUTO to determine best number of threads.
6 SYM+I 10106.619 15 20243.238 20243.440 20329.911
WARNING: Number of threads seems too high for short alignments. Use -T AUTO to determine best number of threads.
7 SYM+G4 10109.264 15 20248.529 20248.731 20335.202
WARNING: Number of threads seems too high for short alignments. Use -T AUTO to determine best number of threads.
8 SYM+I+G4 10105.978 16 20243.957 20244.186 20336.408
WARNING: Number of threads seems too high for short alignments. Use -T AUTO to determine best number of threads.
10 TVM+F+I 9969.542 17 19973.084 19973.343 20071.314
WARNING: Number of threads seems too high for short alignments. Use -T AUTO to determine best number of threads.
11 TVM+F+G4 9970.077 17 19974.155 19974.413 20072.384
WARNING: Number of threads seems too high for short alignments. Use -T AUTO to determine best number of threads.
12 TVM+F+I+G4 9968.124 18 19972.249 19972.537 20076.256
WARNING: Number of threads seems too high for short alignments. Use -T AUTO to determine best number of threads.
14 TVMe+I 10112.050 14 20252.100 20252.277 20332.995
WARNING: Number of threads seems too high for short alignments. Use -T AUTO to determine best number of threads.
15 TVMe+G4 10115.760 14 20259.521 20259.698 20340.416
WARNING: Number of threads seems too high for short alignments. Use -T AUTO to determine best number of threads.
16 TVMe+I+G4 10112.239 15 20254.478 20254.680 20341.151
WARNING: Number of threads seems too high for short alignments. Use -T AUTO to determine best number of threads.
18 TIM3+F+I 10004.794 16 20041.588 20041.817 20134.039
WARNING: Number of threads seems too high for short alignments. Use -T AUTO to determine best number of threads.
19 TIM3+F+G4 10003.134 16 20038.269 20038.498 20130.720
WARNING: Number of threads seems too high for short alignments. Use -T AUTO to determine best number of threads.
20 TIM3+F+I+G4 10001.831 17 20037.662 20037.920 20135.892
WARNING: Number of threads seems too high for short alignments. Use -T AUTO to determine best number of threads.
22 TIM3e+I 10233.779 13 20493.557 20493.711 20568.674
WARNING: Number of threads seems too high for short alignments. Use -T AUTO to determine best number of threads.
23 TIM3e+G4 10234.984 13 20495.968 20496.121 20571.085
WARNING: Number of threads seems too high for short alignments. Use -T AUTO to determine best number of threads.
24 TIM3e+I+G4 10233.164 14 20494.327 20494.504 20575.222
WARNING: Number of threads seems too high for short alignments. Use -T AUTO to determine best number of threads.
26 TIM2+F+I 9960.089 16 19952.178 19952.407 20044.629
WARNING: Number of threads seems too high for short alignments. Use -T AUTO to determine best number of threads.
27 TIM2+F+G4 9958.889 16 19949.778 19950.007 20042.229
WARNING: Number of threads seems too high for short alignments. Use -T AUTO to determine best number of threads.
28 TIM2+F+I+G4 9956.690 17 19947.381 19947.639 20045.610
WARNING: Number of threads seems too high for short alignments. Use -T AUTO to determine best number of threads.
30 TIM2e+I 10159.736 13 20345.473 20345.626 20420.589
WARNING: Number of threads seems too high for short alignments. Use -T AUTO to determine best number of threads.
31 TIM2e+G4 10166.496 13 20358.992 20359.145 20434.109
WARNING: Number of threads seems too high for short alignments. Use -T AUTO to determine best number of threads.
32 TIM2e+I+G4 10162.604 14 20353.209 20353.386 20434.104
WARNING: Number of threads seems too high for short alignments. Use -T AUTO to determine best number of threads.
34 TIM+F+I 9978.268 16 19988.535 19988.765 20080.987
WARNING: Number of threads seems too high for short alignments. Use -T AUTO to determine best number of threads.
35 TIM+F+G4 9976.342 16 19984.683 19984.913 20077.135
WARNING: Number of threads seems too high for short alignments. Use -T AUTO to determine best number of threads.
36 TIM+F+I+G4 9974.947 17 19983.894 19984.152 20082.123
WARNING: Number of threads seems too high for short alignments. Use -T AUTO to determine best number of threads.
38 TIMe+I 10187.704 13 20401.408 20401.562 20476.525
WARNING: Number of threads seems too high for short alignments. Use -T AUTO to determine best number of threads.
39 TIMe+G4 10195.091 13 20416.182 20416.335 20491.298
WARNING: Number of threads seems too high for short alignments. Use -T AUTO to determine best number of threads.
40 TIMe+I+G4 10192.910 14 20413.821 20413.998 20494.716
WARNING: Number of threads seems too high for short alignments. Use -T AUTO to determine best number of threads.
42 TPM3u+F+I 10019.385 15 20068.770 20068.972 20155.443
WARNING: Number of threads seems too high for short alignments. Use -T AUTO to determine best number of threads.
43 TPM3u+F+G4 10022.668 15 20075.336 20075.538 20162.009
WARNING: Number of threads seems too high for short alignments. Use -T AUTO to determine best number of threads.
44 TPM3u+F+I+G4 10021.313 16 20074.626 20074.855 20167.077
WARNING: Number of threads seems too high for short alignments. Use -T AUTO to determine best number of threads.
46 TPM3+I 10240.588 12 20505.176 20505.307 20574.515
WARNING: Number of threads seems too high for short alignments. Use -T AUTO to determine best number of threads.
47 TPM3+G4 10246.096 12 20516.192 20516.324 20585.531
WARNING: Number of threads seems too high for short alignments. Use -T AUTO to determine best number of threads.
48 TPM3+I+G4 10243.636 13 20513.272 20513.425 20588.389
WARNING: Number of threads seems too high for short alignments. Use -T AUTO to determine best number of threads.
50 TPM2u+F+I 9976.669 15 19983.337 19983.540 20070.011
WARNING: Number of threads seems too high for short alignments. Use -T AUTO to determine best number of threads.
51 TPM2u+F+G4 9978.794 15 19987.588 19987.790 20074.261
WARNING: Number of threads seems too high for short alignments. Use -T AUTO to determine best number of threads.
52 TPM2u+F+I+G4 9976.786 16 19985.571 19985.801 20078.023
WARNING: Number of threads seems too high for short alignments. Use -T AUTO to determine best number of threads.
54 TPM2+I 10164.413 12 20352.827 20352.958 20422.165
WARNING: Number of threads seems too high for short alignments. Use -T AUTO to determine best number of threads.
55 TPM2+G4 10171.099 12 20366.199 20366.330 20435.538
WARNING: Number of threads seems too high for short alignments. Use -T AUTO to determine best number of threads.
56 TPM2+I+G4 10167.174 13 20360.347 20360.500 20435.464
WARNING: Number of threads seems too high for short alignments. Use -T AUTO to determine best number of threads.
58 K3Pu+F+I 9994.574 15 20019.149 20019.351 20105.822
WARNING: Number of threads seems too high for short alignments. Use -T AUTO to determine best number of threads.
59 K3Pu+F+G4 9997.747 15 20025.495 20025.697 20112.168
WARNING: Number of threads seems too high for short alignments. Use -T AUTO to determine best number of threads.
60 K3Pu+F+I+G4 9996.293 16 20024.586 20024.816 20117.038
WARNING: Number of threads seems too high for short alignments. Use -T AUTO to determine best number of threads.
62 K3P+I 10193.175 12 20410.349 20410.480 20479.688
WARNING: Number of threads seems too high for short alignments. Use -T AUTO to determine best number of threads.
63 K3P+G4 10203.234 12 20430.468 20430.600 20499.807
WARNING: Number of threads seems too high for short alignments. Use -T AUTO to determine best number of threads.
64 K3P+I+G4 10200.723 13 20427.446 20427.600 20502.563
WARNING: Number of threads seems too high for short alignments. Use -T AUTO to determine best number of threads.
66 TN+F+I 10005.761 15 20041.522 20041.724 20128.195
WARNING: Number of threads seems too high for short alignments. Use -T AUTO to determine best number of threads.
67 TN+F+G4 10003.782 15 20037.564 20037.767 20124.237
WARNING: Number of threads seems too high for short alignments. Use -T AUTO to determine best number of threads.
68 TN+F+I+G4 10002.313 16 20036.626 20036.856 20129.078
WARNING: Number of threads seems too high for short alignments. Use -T AUTO to determine best number of threads.
70 TNe+I 10266.205 12 20556.409 20556.541 20625.748
WARNING: Number of threads seems too high for short alignments. Use -T AUTO to determine best number of threads.
71 TNe+G4 10273.280 12 20570.561 20570.692 20639.899
WARNING: Number of threads seems too high for short alignments. Use -T AUTO to determine best number of threads.
72 TNe+I+G4 10271.035 13 20568.070 20568.223 20643.186
WARNING: Number of threads seems too high for short alignments. Use -T AUTO to determine best number of threads.
74 HKY+F+I 10020.421 14 20068.842 20069.019 20149.737
WARNING: Number of threads seems too high for short alignments. Use -T AUTO to determine best number of threads.
75 HKY+F+G4 10023.678 14 20075.356 20075.533 20156.251
WARNING: Number of threads seems too high for short alignments. Use -T AUTO to determine best number of threads.
76 HKY+F+I+G4 10022.196 15 20074.393 20074.595 20161.066
WARNING: Number of threads seems too high for short alignments. Use -T AUTO to determine best number of threads.
78 K2P+I 10272.035 11 20566.071 20566.182 20629.631
WARNING: Number of threads seems too high for short alignments. Use -T AUTO to determine best number of threads.
79 K2P+G4 10281.744 11 20585.488 20585.599 20649.049
WARNING: Number of threads seems too high for short alignments. Use -T AUTO to determine best number of threads.
80 K2P+I+G4 10279.249 12 20582.498 20582.630 20651.837
WARNING: Number of threads seems too high for short alignments. Use -T AUTO to determine best number of threads.
82 F81+F+I 10041.407 13 20108.815 20108.968 20183.932
WARNING: Number of threads seems too high for short alignments. Use -T AUTO to determine best number of threads.
83 F81+F+G4 10046.374 13 20118.748 20118.901 20193.865
WARNING: Number of threads seems too high for short alignments. Use -T AUTO to determine best number of threads.
84 F81+F+I+G4 10044.860 14 20117.720 20117.897 20198.615
WARNING: Number of threads seems too high for short alignments. Use -T AUTO to determine best number of threads.
86 JC+I 10275.298 10 20570.596 20570.689 20628.378
WARNING: Number of threads seems too high for short alignments. Use -T AUTO to determine best number of threads.
87 JC+G4 10285.852 10 20591.704 20591.796 20649.486
WARNING: Number of threads seems too high for short alignments. Use -T AUTO to determine best number of threads.
88 JC+I+G4 10283.324 11 20588.649 20588.760 20652.209
Akaike Information Criterion: GTR+F+I+G4
Corrected Akaike Information Criterion: GTR+F+I+G4
Bayesian Information Criterion: GTR+F+G4
Best-fit model: GTR+F+G4 chosen according to BIC
All model information printed to results/supermatrix/supermatrix.cds.fa.model.gz
CPU time for ModelFinder: 2560.821 seconds (0h:42m:40s)
Wall-clock time for ModelFinder: 213.459 seconds (0h:3m:33s)
Generating 1000 samples for ultrafast bootstrap (seed: 161615)...
NOTE: 2 MB RAM (0 GB) is required!
WARNING: Number of threads seems too high for short alignments. Use -T AUTO to determine best number of threads.
Estimate model parameters (epsilon = 0.100)
1. Initial log-likelihood: -9950.622
Optimal log-likelihood: -9950.621
Rate parameters: A-C: 2.64999 A-G: 2.93589 A-T: 3.95010 C-G: 1.95186 C-T: 6.16638 G-T: 1.00000
Base frequencies: A: 0.327 C: 0.159 G: 0.195 T: 0.319
Gamma shape alpha: 0.395
Parameters optimization took 1 rounds (0.701 sec)
Wrote distance file to...
Computing ML distances based on estimated model parameters...
Calculating distance matrix: done in 0.00680771 secs using 1641% CPU
Computing ML distances took 0.038560 sec (of wall-clock time) 0.407615 sec (of CPU time)
Setting up auxiliary I and S matrices: done in 0.0125567 secs using 125.4% CPU
Constructing RapidNJ tree: done in 0.0326775 secs
Computing RapidNJ tree took 0.045494 sec (of wall-clock time) 0.019727 sec (of CPU time)
Log-likelihood of RapidNJ tree: -9985.567
--------------------------------------------------------------------
| INITIALIZING CANDIDATE TREE SET |
--------------------------------------------------------------------
Generating 98 parsimony trees... 0.036 second
Computing log-likelihood of 5 initial trees ... 1.796 seconds
Current best score: -9950.621
Do NNI search on 7 best initial trees
Optimizing NNI: done in 1.07794 secs using 1320% CPU
Optimizing NNI: done in 4.34915 secs using 823.7% CPU
Optimizing NNI: done in 1.9475 secs using 1719% CPU
Optimizing NNI: done in 1.38306 secs using 1540% CPU
Optimizing NNI: done in 0.128873 secs using 1496% CPU
Optimizing NNI: done in 2.7676 secs using 1134% CPU
Optimizing NNI: done in 1.61927 secs using 2118% CPU
Finish initializing candidate tree set (7)
Current best tree score: -9950.621 / CPU time: 15.424
Number of iterations: 7
--------------------------------------------------------------------
| OPTIMIZING CANDIDATE TREE SET |
--------------------------------------------------------------------
Optimizing NNI: done in 1.2637 secs using 2331% CPU
Optimizing NNI: done in 1.25443 secs using 2252% CPU
Optimizing NNI: done in 1.24538 secs using 2669% CPU
Iteration 10 / LogL: -9950.844 / Time: 0h:0m:21s
Optimizing NNI: done in 1.29607 secs using 2272% CPU
Optimizing NNI: done in 0.51465 secs using 2616% CPU
Optimizing NNI: done in 1.12706 secs using 2781% CPU
UPDATE BEST LOG-LIKELIHOOD: -9950.621
Optimizing NNI: done in 1.22644 secs using 2840% CPU
Optimizing NNI: done in 2.03725 secs using 2933% CPU
Optimizing NNI: done in 1.23451 secs using 2816% CPU
Optimizing NNI: done in 1.26577 secs using 2534% CPU
Optimizing NNI: done in 2.00597 secs using 2854% CPU
Optimizing NNI: done in 0.1121 secs using 2942% CPU
Optimizing NNI: done in 1.94325 secs using 2761% CPU
Iteration 20 / LogL: -9950.638 / Time: 0h:0m:34s
Optimizing NNI: done in 1.25501 secs using 2649% CPU
Optimizing NNI: done in 1.10358 secs using 2628% CPU
UPDATE BEST LOG-LIKELIHOOD: -9950.621
Optimizing NNI: done in 1.24876 secs using 2637% CPU
Optimizing NNI: done in 1.07974 secs using 2687% CPU
Optimizing NNI: done in 1.06359 secs using 2647% CPU
Optimizing NNI: done in 1.09765 secs using 2338% CPU
UPDATE BEST LOG-LIKELIHOOD: -9950.621
Optimizing NNI: done in 1.92631 secs using 2718% CPU
Optimizing NNI: done in 1.2097 secs using 2955% CPU
Optimizing NNI: done in 1.16211 secs using 2921% CPU
Optimizing NNI: done in 0.495309 secs using 2979% CPU
Iteration 30 / LogL: -9960.717 / Time: 0h:0m:45s (0h:1m:50s left)
Optimizing NNI: done in 0.505813 secs using 2938% CPU
Optimizing NNI: done in 1.90804 secs using 2650% CPU
Optimizing NNI: done in 1.16779 secs using 2573% CPU
Optimizing NNI: done in 1.94331 secs using 2939% CPU
Optimizing NNI: done in 1.60375 secs using 2984% CPU
Optimizing NNI: done in 0.495241 secs using 2997% CPU
Optimizing NNI: done in 1.06242 secs using 2898% CPU
Optimizing NNI: done in 1.25887 secs using 2648% CPU
Optimizing NNI: done in 1.2501 secs using 2670% CPU
Optimizing NNI: done in 1.19824 secs using 2672% CPU
Iteration 40 / LogL: -9950.646 / Time: 0h:0m:58s (0h:1m:30s left)
Optimizing NNI: done in 1.92262 secs using 2556% CPU
Optimizing NNI: done in 1.2263 secs using 2404% CPU
Optimizing NNI: done in 1.1602 secs using 2967% CPU
Optimizing NNI: done in 1.16783 secs using 2928% CPU
Optimizing NNI: done in 0.566042 secs using 2926% CPU
Optimizing NNI: done in 1.79761 secs using 2936% CPU
Optimizing NNI: done in 0.213822 secs using 3031% CPU
Optimizing NNI: done in 1.93768 secs using 2473% CPU
Optimizing NNI: done in 1.20909 secs using 2882% CPU
Optimizing NNI: done in 1.12051 secs using 2918% CPU
Iteration 50 / LogL: -9950.629 / Time: 0h:1m:11s (0h:1m:12s left)
Log-likelihood cutoff on original alignment: -9981.047
Optimizing NNI: done in 0.842645 secs using 2953% CPU
Optimizing NNI: done in 1.17608 secs using 2930% CPU
Optimizing NNI: done in 1.11613 secs using 2955% CPU
Optimizing NNI: done in 1.21222 secs using 2674% CPU
Optimizing NNI: done in 1.05147 secs using 2679% CPU
Optimizing NNI: done in 1.94104 secs using 2686% CPU
Optimizing NNI: done in 2.08926 secs using 2435% CPU
Optimizing NNI: done in 1.18808 secs using 2650% CPU
Optimizing NNI: done in 0.493154 secs using 2967% CPU
Optimizing NNI: done in 1.17491 secs using 2909% CPU
Iteration 60 / LogL: -9950.646 / Time: 0h:1m:23s (0h:0m:56s left)
Optimizing NNI: done in 0.351238 secs using 2965% CPU
Optimizing NNI: done in 1.94391 secs using 2932% CPU
Optimizing NNI: done in 1.23189 secs using 2708% CPU
Optimizing NNI: done in 2.09152 secs using 2586% CPU
Optimizing NNI: done in 1.89626 secs using 2939% CPU
Optimizing NNI: done in 1.16286 secs using 2946% CPU
Optimizing NNI: done in 1.15525 secs using 2959% CPU
Optimizing NNI: done in 0.520634 secs using 2725% CPU
Optimizing NNI: done in 1.21722 secs using 2623% CPU
Optimizing NNI: done in 1.95423 secs using 2658% CPU
Iteration 70 / LogL: -9950.638 / Time: 0h:1m:37s (0h:0m:42s left)
Optimizing NNI: done in 1.08009 secs using 2667% CPU
Optimizing NNI: done in 2.00654 secs using 2387% CPU
Optimizing NNI: done in 1.91199 secs using 2851% CPU
Optimizing NNI: done in 0.491389 secs using 2974% CPU
Optimizing NNI: done in 1.20929 secs using 2941% CPU
Optimizing NNI: done in 1.20065 secs using 2973% CPU
Optimizing NNI: done in 0.577667 secs using 2944% CPU
Optimizing NNI: done in 2.11667 secs using 2434% CPU
Optimizing NNI: done in 1.8466 secs using 2956% CPU
Optimizing NNI: done in 0.488527 secs using 2922% CPU
Iteration 80 / LogL: -9971.306 / Time: 0h:1m:50s (0h:0m:27s left)
Optimizing NNI: done in 1.1698 secs using 2945% CPU
Optimizing NNI: done in 1.21815 secs using 2959% CPU
Optimizing NNI: done in 0.50812 secs using 2877% CPU
Optimizing NNI: done in 1.19092 secs using 2691% CPU
Optimizing NNI: done in 0.51549 secs using 2688% CPU
Optimizing NNI: done in 2.04443 secs using 2661% CPU
Optimizing NNI: done in 1.22694 secs using 2674% CPU
Optimizing NNI: done in 1.93917 secs using 2382% CPU
Optimizing NNI: done in 1.22256 secs using 2937% CPU
Optimizing NNI: done in 1.63885 secs using 2948% CPU
Iteration 90 / LogL: -9950.971 / Time: 0h:2m:3s (0h:0m:13s left)
Optimizing NNI: done in 0.471577 secs using 3040% CPU
Optimizing NNI: done in 1.8703 secs using 2962% CPU
Optimizing NNI: done in 1.31571 secs using 2207% CPU
Optimizing NNI: done in 0.774541 secs using 2930% CPU
Optimizing NNI: done in 1.19238 secs using 2977% CPU
Optimizing NNI: done in 1.15221 secs using 2891% CPU
Optimizing NNI: done in 1.85709 secs using 2969% CPU
Optimizing NNI: done in 1.2023 secs using 2789% CPU
Optimizing NNI: done in 1.20508 secs using 2657% CPU
Optimizing NNI: done in 1.20611 secs using 2659% CPU
Iteration 100 / LogL: -9950.648 / Time: 0h:2m:16s (0h:0m:0s left)
Log-likelihood cutoff on original alignment: -9981.047
NOTE: Bootstrap correlation coefficient of split occurrence frequencies: 1.000
Optimizing NNI: done in 1.96446 secs using 2679% CPU
TREE SEARCH COMPLETED AFTER 101 ITERATIONS / Time: 0h:2m:18s
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| FINALIZING TREE SEARCH |
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Performs final model parameters optimization
Estimate model parameters (epsilon = 0.010)
1. Initial log-likelihood: -9950.621
Optimal log-likelihood: -9950.620
Rate parameters: A-C: 2.65045 A-G: 2.95002 A-T: 3.94530 C-G: 1.95408 C-T: 6.17521 G-T: 1.00000
Base frequencies: A: 0.327 C: 0.159 G: 0.195 T: 0.319
Gamma shape alpha: 0.395
Parameters optimization took 1 rounds (0.317 sec)
BEST SCORE FOUND : -9950.620
Creating bootstrap support values...
Split supports printed to NEXUS file results/supermatrix/supermatrix.cds.fa.splits.nex
Total tree length: 1.086
Total number of iterations: 101
CPU time used for tree search: 3503.100 sec (0h:58m:23s)
Wall-clock time used for tree search: 136.261 sec (0h:2m:16s)
Total CPU time used: 3534.349 sec (0h:58m:54s)
Total wall-clock time used: 138.369 sec (0h:2m:18s)
Computing bootstrap consensus tree...
Reading input file results/supermatrix/supermatrix.cds.fa.splits.nex...
6 taxa and 11 splits.
Consensus tree written to results/supermatrix/supermatrix.cds.fa.contree
Reading input trees file results/supermatrix/supermatrix.cds.fa.contree
Log-likelihood of consensus tree: -9950.620
Analysis results written to:
IQ-TREE report: results/supermatrix/supermatrix.cds.fa.iqtree
Maximum-likelihood tree: results/supermatrix/supermatrix.cds.fa.treefile
Likelihood distances: results/supermatrix/supermatrix.cds.fa.mldist
Ultrafast bootstrap approximation results written to:
Split support values: results/supermatrix/supermatrix.cds.fa.splits.nex
Consensus tree: results/supermatrix/supermatrix.cds.fa.contree
Screen log file: results/supermatrix/supermatrix.cds.fa.log
ALISIM COMMAND
--------------
--alisim simulated_MSA -t results/supermatrix/supermatrix.cds.fa.treefile -m "GTR{2.65045,2.95002,3.9453,1.95408,6.17521}+F{0.327341,0.1587,0.195008,0.318951}+G4{0.394866}" --length 2388
Date and Time: Sat Dec 16 03:48:38 2023
Gene Tree
OG0000004
IQ-TREE 2.2.0.3 COVID-edition built Aug 2 2022 Input file name: results/alignment/trimmed_cds/OG0000004.trimmed.cds.alignment.fa Type of analysis: ModelFinder + tree reconstruction + ultrafast bootstrap (1000 replicates) Random seed number: 257855 REFERENCES ---------- To cite IQ-TREE please use: Bui Quang Minh, Heiko A. Schmidt, Olga Chernomor, Dominik Schrempf, Michael D. Woodhams, Arndt von Haeseler, and Robert Lanfear (2020) IQ-TREE 2: New models and efficient methods for phylogenetic inference in the genomic era. Mol. Biol. Evol., in press. https://doi.org/10.1093/molbev/msaa015 To cite ModelFinder please use: Subha Kalyaanamoorthy, Bui Quang Minh, Thomas KF Wong, Arndt von Haeseler, and Lars S Jermiin (2017) ModelFinder: Fast model selection for accurate phylogenetic estimates. Nature Methods, 14:587–589. https://doi.org/10.1038/nmeth.4285 Since you used ultrafast bootstrap (UFBoot) please also cite: Diep Thi Hoang, Olga Chernomor, Arndt von Haeseler, Bui Quang Minh, and Le Sy Vinh (2018) UFBoot2: Improving the ultrafast bootstrap approximation. Mol. Biol. Evol., 35:518–522. https://doi.org/10.1093/molbev/msx281 SEQUENCE ALIGNMENT ------------------ Input data: 6 sequences with 1425 nucleotide sites Number of constant sites: 945 (= 66.3158% of all sites) Number of invariant (constant or ambiguous constant) sites: 945 (= 66.3158% of all sites) Number of parsimony informative sites: 247 Number of distinct site patterns: 273 ModelFinder ----------- Best-fit model according to BIC: GTR+F+G4 List of models sorted by BIC scores: Model LogL AIC w-AIC AICc w-AICc BIC w-BIC GTR+F+G4 -5313.239 10662.478 + 0.637 10662.964 + 0.643 10757.193 + 0.902 GTR+F+I -5315.864 10667.729 - 0.0462 10668.215 - 0.0465 10762.444 + 0.0653 GTR+F+I+G4 -5312.939 10663.878 + 0.316 10664.419 + 0.311 10763.855 - 0.0323 SYM+G4 -5373.519 10777.038 - 8.47e-26 10777.379 - 9.19e-26 10855.967 - 3.21e-22 SYM+I -5373.847 10777.694 - 6.1e-26 10778.035 - 6.62e-26 10856.623 - 2.31e-22 SYM+I+G4 -5373.088 10778.176 - 4.8e-26 10778.562 - 5.09e-26 10862.367 - 1.31e-23 HKY+F+I -5389.886 10807.772 - 1.8e-32 10808.070 - 1.99e-32 10881.439 - 9.45e-28 HKY+F+G4 -5391.663 10811.326 - 3.04e-33 10811.624 - 3.37e-33 10884.993 - 1.6e-28 HKY+F+I+G4 -5392.647 10815.295 - 4.17e-34 10815.635 - 4.53e-34 10894.224 - 1.58e-30 F81+F+I -5407.874 10841.748 - 7.52e-40 10842.006 - 8.51e-40 10910.153 - 5.5e-34 F81+F+G4 -5410.576 10847.151 - 5.05e-41 10847.409 - 5.71e-41 10915.556 - 3.69e-35 F81+F+I+G4 -5411.633 10851.266 - 6.45e-42 10851.564 - 7.15e-42 10924.933 - 3.4e-37 GTR+F -5462.059 10958.118 - 4.05e-65 10958.553 - 4.19e-65 11047.570 - 7.96e-64 K2P+I -5487.031 10996.062 - 2.33e-73 10996.249 - 2.73e-73 11053.943 - 3.29e-65 JC+I -5493.624 11007.248 - 8.68e-76 11007.404 - 1.03e-75 11059.868 - 1.7e-66 K2P+G4 -5491.147 11004.293 - 3.8e-75 11004.480 - 4.46e-75 11062.175 - 5.36e-67 JC+G4 -5498.419 11016.839 - 7.18e-78 11016.994 - 8.54e-78 11069.458 - 1.41e-68 K2P+I+G4 -5492.024 11008.048 - 5.82e-76 11008.269 - 6.7e-76 11071.191 - 5.91e-69 JC+I+G4 -5499.410 11020.820 - 9.8e-79 11021.007 - 1.15e-78 11078.702 - 1.38e-70 AIC, w-AIC : Akaike information criterion scores and weights. AICc, w-AICc : Corrected AIC scores and weights. BIC, w-BIC : Bayesian information criterion scores and weights. Plus signs denote the 95% confidence sets. Minus signs denote significant exclusion. SUBSTITUTION PROCESS -------------------- Model of substitution: GTR+F+G4 Rate parameter R: A-C: 1.9031 A-G: 2.4911 A-T: 4.8036 C-G: 1.1492 C-T: 7.7336 G-T: 1.0000 State frequencies: (empirical counts from alignment) pi(A) = 0.2978 pi(C) = 0.1621 pi(G) = 0.2254 pi(T) = 0.3147 Rate matrix Q: A -0.9788 0.1268 0.2307 0.6213 C 0.2329 -1.34 0.1064 1 G 0.3048 0.07655 -0.5107 0.1293 T 0.5878 0.5152 0.09262 -1.196 Model of rate heterogeneity: Gamma with 4 categories Gamma shape alpha: 0.3265 Category Relative_rate Proportion 1 0.007692 0.25 2 0.1252 0.25 3 0.6378 0.25 4 3.229 0.25 Relative rates are computed as MEAN of the portion of the Gamma distribution falling in the category. MAXIMUM LIKELIHOOD TREE ----------------------- Log-likelihood of the tree: -5313.2364 (s.e. 110.0860) Unconstrained log-likelihood (without tree): -4731.2277 Number of free parameters (#branches + #model parameters): 18 Akaike information criterion (AIC) score: 10662.4728 Corrected Akaike information criterion (AICc) score: 10662.9593 Bayesian information criterion (BIC) score: 10757.1875 Total tree length (sum of branch lengths): 0.7900 Sum of internal branch lengths: 0.1578 (19.9696% of tree length) NOTE: Tree is UNROOTED although outgroup taxon 'Derbesia_sp_WEST4838' is drawn at root Numbers in parentheses are ultrafast bootstrap support (%) +------------------------------Derbesia_sp_WEST4838 | | +-----------------------------Caulerpa_cliftonii_HV03798 | +------------| (95) | | | +---------------Chlorodesmis_fastigiata_HV03865 | | +----------| (98) | | +-----------------Flabellia_petiolata_HV01202 +--------------| (100) | +---------------------------------------Avrainvillea_mazei_HV02664 | +--------------------------Bryopsis_plumosa_WEST4718 Tree in newick format: (Derbesia_sp_WEST4838:0.1213215206,((Caulerpa_cliftonii_HV03798:0.1170328192,(Chlorodesmis_fastigiata_HV03865:0.0625957226,Flabellia_petiolata_HV01202:0.0719046281)98:0.0452561871)95:0.0513217712,Avrainvillea_mazei_HV02664:0.1543734239)100:0.0611901346,Bryopsis_plumosa_WEST4718:0.1050465397); CONSENSUS TREE -------------- Consensus tree is constructed from 1000 bootstrap trees Log-likelihood of consensus tree: -5313.236393 Robinson-Foulds distance between ML tree and consensus tree: 0 Branches with support >0.000000% are kept (extended consensus) Branch lengths are optimized by maximum likelihood on original alignment Numbers in parentheses are bootstrap supports (%) +------------------------------Derbesia_sp_WEST4838 | | +-----------------------------Caulerpa_cliftonii_HV03798 | +------------| (95) | | | +---------------Chlorodesmis_fastigiata_HV03865 | | +----------| (98) | | +-----------------Flabellia_petiolata_HV01202 +--------------| (100) | +---------------------------------------Avrainvillea_mazei_HV02664 | +--------------------------Bryopsis_plumosa_WEST4718 Consensus tree in newick format: (Derbesia_sp_WEST4838:0.1213215379,((Caulerpa_cliftonii_HV03798:0.1170336988,(Chlorodesmis_fastigiata_HV03865:0.0625985454,Flabellia_petiolata_HV01202:0.0718943603)98:0.0452466890)95:0.0513171139,Avrainvillea_mazei_HV02664:0.1543670772)100:0.0611902467,Bryopsis_plumosa_WEST4718:0.1050435458); TIME STAMP ---------- Date and time: Sat Dec 16 03:42:29 2023 Total CPU time used: 0.965507 seconds (0h:0m:0s) Total wall-clock time used: 1.692147754 seconds (0h:0m:1s)
IQ-TREE multicore version 2.2.0.3 COVID-edition for Linux 64-bit built Aug 2 2022
Developed by Bui Quang Minh, James Barbetti, Nguyen Lam Tung,
Olga Chernomor, Heiko Schmidt, Dominik Schrempf, Michael Woodhams, Ly Trong Nhan.
Host: herbairumphylo (AVX512, FMA3, 283 GB RAM)
Command: iqtree2 -s results/alignment/trimmed_cds/OG0000004.trimmed.cds.alignment.fa -bb 1000 -m TEST -nt 1 -mset mrbayes -pre results/gene_tree/OG0000004/OG0000004.cds -redo
Seed: 257855 (Using SPRNG - Scalable Parallel Random Number Generator)
Time: Sat Dec 16 03:42:27 2023
Kernel: AVX+FMA - 1 threads (32 CPU cores detected)
HINT: Use -nt option to specify number of threads because your CPU has 32 cores!
HINT: -nt AUTO will automatically determine the best number of threads to use.
Reading alignment file results/alignment/trimmed_cds/OG0000004.trimmed.cds.alignment.fa ... Fasta format detected
Reading fasta file: done in 0.000224255 secs using 99.44% CPU
Alignment most likely contains DNA/RNA sequences
Constructing alignment: done in 0.00139315 secs using 27.35% CPU
Alignment has 6 sequences with 1425 columns, 273 distinct patterns
247 parsimony-informative, 233 singleton sites, 944 constant sites
Gap/Ambiguity Composition p-value
Analyzing sequences: done in 1.07959e-05 secs
1 Derbesia_sp_WEST4838 0.00% passed 97.69%
2 Caulerpa_cliftonii_HV03798 0.00% passed 49.86%
3 Avrainvillea_mazei_HV02664 0.00% passed 77.46%
4 Chlorodesmis_fastigiata_HV03865 0.00% passed 84.52%
5 Flabellia_petiolata_HV01202 0.00% passed 89.25%
6 Bryopsis_plumosa_WEST4718 0.00% passed 88.27%
**** TOTAL 0.00% 0 sequences failed composition chi2 test (p-value<5%; df=3)
Checking for duplicate sequences: done in 2.39462e-05 secs
Create initial parsimony tree by phylogenetic likelihood library (PLL)... 0.000 seconds
Perform fast likelihood tree search using GTR+I+G model...
Estimate model parameters (epsilon = 5.000)
Perform nearest neighbor interchange...
Optimizing NNI: done in 0.00129852 secs using 85.56% CPU
Estimate model parameters (epsilon = 1.000)
1. Initial log-likelihood: -5312.975
Optimal log-likelihood: -5312.962
Rate parameters: A-C: 1.89811 A-G: 2.47143 A-T: 4.82573 C-G: 1.13587 C-T: 7.79940 G-T: 1.00000
Base frequencies: A: 0.298 C: 0.162 G: 0.225 T: 0.315
Proportion of invariable sites: 0.331
Gamma shape alpha: 0.791
Parameters optimization took 1 rounds (0.002 sec)
Time for fast ML tree search: 0.046 seconds
NOTE: ModelFinder requires 1 MB RAM!
ModelFinder will test up to 24 DNA models (sample size: 1425) ...
No. Model -LnL df AIC AICc BIC
1 GTR+F 5462.059 17 10958.118 10958.553 11047.570
2 GTR+F+I 5315.864 18 10667.729 10668.215 10762.444
3 GTR+F+G4 5313.239 18 10662.478 10662.964 10757.193
4 GTR+F+I+G4 5312.939 19 10663.878 10664.419 10763.855
6 SYM+I 5373.847 15 10777.694 10778.035 10856.623
7 SYM+G4 5373.519 15 10777.038 10777.379 10855.967
8 SYM+I+G4 5373.088 16 10778.176 10778.562 10862.367
10 HKY+F+I 5389.886 14 10807.772 10808.070 10881.439
11 HKY+F+G4 5391.663 14 10811.326 10811.624 10884.993
12 HKY+F+I+G4 5392.647 15 10815.295 10815.635 10894.224
14 K2P+I 5487.031 11 10996.062 10996.249 11053.943
15 K2P+G4 5491.147 11 11004.293 11004.480 11062.175
16 K2P+I+G4 5492.024 12 11008.048 11008.269 11071.191
18 F81+F+I 5407.874 13 10841.748 10842.006 10910.153
19 F81+F+G4 5410.576 13 10847.151 10847.409 10915.556
20 F81+F+I+G4 5411.633 14 10851.266 10851.564 10924.933
22 JC+I 5493.624 10 11007.248 11007.404 11059.868
23 JC+G4 5498.419 10 11016.839 11016.994 11069.458
24 JC+I+G4 5499.410 11 11020.820 11021.007 11078.702
Akaike Information Criterion: GTR+F+G4
Corrected Akaike Information Criterion: GTR+F+G4
Bayesian Information Criterion: GTR+F+G4
Best-fit model: GTR+F+G4 chosen according to BIC
All model information printed to results/gene_tree/OG0000004/OG0000004.cds.model.gz
CPU time for ModelFinder: 0.130 seconds (0h:0m:0s)
Wall-clock time for ModelFinder: 0.287 seconds (0h:0m:0s)
Generating 1000 samples for ultrafast bootstrap (seed: 257855)...
NOTE: 1 MB RAM (0 GB) is required!
Estimate model parameters (epsilon = 0.100)
1. Initial log-likelihood: -5313.239
Optimal log-likelihood: -5313.237
Rate parameters: A-C: 1.90706 A-G: 2.48432 A-T: 4.80942 C-G: 1.14890 C-T: 7.71851 G-T: 1.00000
Base frequencies: A: 0.298 C: 0.162 G: 0.225 T: 0.315
Gamma shape alpha: 0.327
Parameters optimization took 1 rounds (0.002 sec)
Wrote distance file to...
Computing ML distances based on estimated model parameters...
Calculating distance matrix: done in 0.000324532 secs using 99.84% CPU
Computing ML distances took 0.000419 sec (of wall-clock time) 0.000406 sec (of CPU time)
Setting up auxiliary I and S matrices: done in 6.45444e-05 secs using 99.16% CPU
Constructing RapidNJ tree: done in 4.62085e-05 secs using 97.38% CPU
Computing RapidNJ tree took 0.000223 sec (of wall-clock time) 0.000196 sec (of CPU time)
Log-likelihood of RapidNJ tree: -5326.194
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| INITIALIZING CANDIDATE TREE SET |
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Generating 98 parsimony trees... 0.062 second
Computing log-likelihood of 5 initial trees ... 0.003 seconds
Current best score: -5313.237
Do NNI search on 7 best initial trees
Optimizing NNI: done in 0.00197581 secs using 99.81% CPU
Optimizing NNI: done in 0.00378162 secs using 99.93% CPU
Optimizing NNI: done in 0.00389465 secs using 99.93% CPU
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Optimizing NNI: done in 0.00382568 secs using 99.93% CPU
Optimizing NNI: done in 0.0199591 secs using 19.75% CPU
Finish initializing candidate tree set (7)
Current best tree score: -5313.237 / CPU time: 0.124
Number of iterations: 7
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| OPTIMIZING CANDIDATE TREE SET |
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Optimizing NNI: done in 0.00347258 secs using 99.93% CPU
UPDATE BEST LOG-LIKELIHOOD: -5313.237
Optimizing NNI: done in 0.00157487 secs using 99.82% CPU
Optimizing NNI: done in 0.00344325 secs using 99.91% CPU
UPDATE BEST LOG-LIKELIHOOD: -5313.237
Iteration 10 / LogL: -5313.237 / Time: 0h:0m:0s
Optimizing NNI: done in 0.00370899 secs using 99.92% CPU
Optimizing NNI: done in 0.00174462 secs using 95.95% CPU
Optimizing NNI: done in 0.0214341 secs using 25.39% CPU
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Iteration 20 / LogL: -5313.428 / Time: 0h:0m:0s
Optimizing NNI: done in 0.00535477 secs using 99.97% CPU
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Optimizing NNI: done in 0.00519586 secs using 99.94% CPU
Iteration 30 / LogL: -5313.322 / Time: 0h:0m:0s (0h:0m:1s left)
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Iteration 40 / LogL: -5319.581 / Time: 0h:0m:0s (0h:0m:1s left)
Optimizing NNI: done in 0.00538877 secs using 99.97% CPU
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Optimizing NNI: done in 0.00542913 secs using 99.96% CPU
Iteration 50 / LogL: -5313.323 / Time: 0h:0m:0s (0h:0m:0s left)
Log-likelihood cutoff on original alignment: -5341.810
Optimizing NNI: done in 0.00357997 secs using 99.92% CPU
Optimizing NNI: done in 0.0214697 secs using 25.49% CPU
Optimizing NNI: done in 0.0054225 secs using 99.95% CPU
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Optimizing NNI: done in 0.0215355 secs using 25.56% CPU
Iteration 60 / LogL: -5313.246 / Time: 0h:0m:1s (0h:0m:0s left)
Optimizing NNI: done in 0.00345656 secs using 99.96% CPU
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Optimizing NNI: done in 0.00157622 secs using 97.39% CPU
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Iteration 70 / LogL: -5313.244 / Time: 0h:0m:1s (0h:0m:0s left)
Optimizing NNI: done in 0.00378656 secs using 92.46% CPU
Optimizing NNI: done in 0.0035195 secs using 96.55% CPU
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Iteration 80 / LogL: -5313.322 / Time: 0h:0m:1s (0h:0m:0s left)
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Iteration 90 / LogL: -5313.299 / Time: 0h:0m:1s (0h:0m:0s left)
Optimizing NNI: done in 0.00359747 secs using 96.12% CPU
Optimizing NNI: done in 0.00559035 secs using 96.52% CPU
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Optimizing NNI: done in 0.00554293 secs using 97.01% CPU
Optimizing NNI: done in 0.00358943 secs using 94.61% CPU
Optimizing NNI: done in 0.00362789 secs using 96.7% CPU
Iteration 100 / LogL: -5313.258 / Time: 0h:0m:1s (0h:0m:0s left)
Log-likelihood cutoff on original alignment: -5341.810
NOTE: Bootstrap correlation coefficient of split occurrence frequencies: 1.000
Optimizing NNI: done in 0.00588131 secs using 92.75% CPU
TREE SEARCH COMPLETED AFTER 101 ITERATIONS / Time: 0h:0m:1s
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| FINALIZING TREE SEARCH |
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Performs final model parameters optimization
Estimate model parameters (epsilon = 0.010)
1. Initial log-likelihood: -5313.237
Optimal log-likelihood: -5313.236
Rate parameters: A-C: 1.90308 A-G: 2.49111 A-T: 4.80363 C-G: 1.14918 C-T: 7.73358 G-T: 1.00000
Base frequencies: A: 0.298 C: 0.162 G: 0.225 T: 0.315
Gamma shape alpha: 0.327
Parameters optimization took 1 rounds (0.002 sec)
BEST SCORE FOUND : -5313.236
Creating bootstrap support values...
Split supports printed to NEXUS file results/gene_tree/OG0000004/OG0000004.cds.splits.nex
Total tree length: 0.790
Total number of iterations: 101
CPU time used for tree search: 0.901 sec (0h:0m:0s)
Wall-clock time used for tree search: 1.555 sec (0h:0m:1s)
Total CPU time used: 0.966 sec (0h:0m:0s)
Total wall-clock time used: 1.683 sec (0h:0m:1s)
Computing bootstrap consensus tree...
Reading input file results/gene_tree/OG0000004/OG0000004.cds.splits.nex...
6 taxa and 15 splits.
Consensus tree written to results/gene_tree/OG0000004/OG0000004.cds.contree
Reading input trees file results/gene_tree/OG0000004/OG0000004.cds.contree
Log-likelihood of consensus tree: -5313.236
Analysis results written to:
IQ-TREE report: results/gene_tree/OG0000004/OG0000004.cds.iqtree
Maximum-likelihood tree: results/gene_tree/OG0000004/OG0000004.cds.treefile
Likelihood distances: results/gene_tree/OG0000004/OG0000004.cds.mldist
Ultrafast bootstrap approximation results written to:
Split support values: results/gene_tree/OG0000004/OG0000004.cds.splits.nex
Consensus tree: results/gene_tree/OG0000004/OG0000004.cds.contree
Screen log file: results/gene_tree/OG0000004/OG0000004.cds.log
ALISIM COMMAND
--------------
--alisim simulated_MSA -t results/gene_tree/OG0000004/OG0000004.cds.treefile -m "GTR{1.90308,2.49111,4.80363,1.14918,7.73358}+F{0.297778,0.162105,0.22538,0.314737}+G4{0.326523}" --length 1425
Date and Time: Sat Dec 16 03:42:29 2023
OG0000000
IQ-TREE 2.2.0.3 COVID-edition built Aug 2 2022 Input file name: results/alignment/trimmed_cds/OG0000000.trimmed.cds.alignment.fa Type of analysis: ModelFinder + tree reconstruction + ultrafast bootstrap (1000 replicates) Random seed number: 255357 REFERENCES ---------- To cite IQ-TREE please use: Bui Quang Minh, Heiko A. Schmidt, Olga Chernomor, Dominik Schrempf, Michael D. Woodhams, Arndt von Haeseler, and Robert Lanfear (2020) IQ-TREE 2: New models and efficient methods for phylogenetic inference in the genomic era. Mol. Biol. Evol., in press. https://doi.org/10.1093/molbev/msaa015 To cite ModelFinder please use: Subha Kalyaanamoorthy, Bui Quang Minh, Thomas KF Wong, Arndt von Haeseler, and Lars S Jermiin (2017) ModelFinder: Fast model selection for accurate phylogenetic estimates. Nature Methods, 14:587–589. https://doi.org/10.1038/nmeth.4285 Since you used ultrafast bootstrap (UFBoot) please also cite: Diep Thi Hoang, Olga Chernomor, Arndt von Haeseler, Bui Quang Minh, and Le Sy Vinh (2018) UFBoot2: Improving the ultrafast bootstrap approximation. Mol. Biol. Evol., 35:518–522. https://doi.org/10.1093/molbev/msx281 SEQUENCE ALIGNMENT ------------------ Input data: 6 sequences with 963 nucleotide sites Number of constant sites: 455 (= 47.2482% of all sites) Number of invariant (constant or ambiguous constant) sites: 455 (= 47.2482% of all sites) Number of parsimony informative sites: 249 Number of distinct site patterns: 334 ModelFinder ----------- Best-fit model according to BIC: HKY+F+G4 List of models sorted by BIC scores: Model LogL AIC w-AIC AICc w-AICc BIC w-BIC HKY+F+G4 -4555.778 9139.556 - 0.00168 9139.999 - 0.00198 9207.737 + 0.769 HKY+F+I+G4 -4554.307 9138.614 - 0.00269 9139.121 - 0.00308 9211.665 + 0.108 HKY+F+I -4557.943 9143.885 - 0.000193 9144.328 - 0.000228 9212.066 + 0.0883 F81+F+G4 -4563.103 9152.205 - 3.01e-06 9152.589 - 3.66e-06 9215.516 - 0.0157 GTR+F+G4 -4546.645 9129.290 + 0.285 9130.015 + 0.292 9216.951 - 0.00768 F81+F+I -4564.150 9154.300 - 1.06e-06 9154.683 - 1.28e-06 9217.610 - 0.00552 F81+F+I+G4 -4561.524 9151.049 - 5.36e-06 9151.492 - 6.33e-06 9219.229 - 0.00246 GTR+F+I -4548.126 9132.253 + 0.0647 9132.977 + 0.0664 9219.914 - 0.00175 GTR+F+I+G4 -4544.825 9127.650 + 0.646 9128.456 + 0.636 9220.181 - 0.00153 GTR+F -4657.034 9348.067 - 8.86e-49 9348.715 - 9.44e-49 9430.858 - 2.73e-49 SYM+I -4671.878 9373.757 - 2.34e-54 9374.264 - 2.67e-54 9446.808 - 9.39e-53 SYM+G4 -4672.933 9375.865 - 8.15e-55 9376.372 - 9.32e-55 9448.916 - 3.27e-53 SYM+I+G4 -4670.387 9372.775 - 3.82e-54 9373.350 - 4.22e-54 9450.696 - 1.34e-53 JC+I -4729.397 9478.793 - 3.64e-77 9479.024 - 4.77e-77 9527.494 - 2.83e-70 JC+G4 -4732.692 9485.384 - 1.35e-78 9485.615 - 1.77e-78 9534.084 - 1.05e-71 K2P+I -4729.392 9480.784 - 1.34e-77 9481.062 - 1.72e-77 9534.355 - 9.16e-72 JC+I+G4 -4730.011 9482.022 - 7.24e-78 9482.300 - 9.28e-78 9535.593 - 4.93e-72 K2P+G4 -4732.683 9487.367 - 5e-79 9487.644 - 6.41e-79 9540.937 - 3.41e-73 K2P+I+G4 -4729.987 9483.975 - 2.73e-78 9484.303 - 3.41e-78 9542.415 - 1.63e-73 AIC, w-AIC : Akaike information criterion scores and weights. AICc, w-AICc : Corrected AIC scores and weights. BIC, w-BIC : Bayesian information criterion scores and weights. Plus signs denote the 95% confidence sets. Minus signs denote significant exclusion. SUBSTITUTION PROCESS -------------------- Model of substitution: HKY+F+G4 Rate parameter R: A-C: 1.0000 A-G: 1.5194 A-T: 1.0000 C-G: 1.0000 C-T: 1.5194 G-T: 1.0000 State frequencies: (empirical counts from alignment) pi(A) = 0.3722 pi(C) = 0.1535 pi(G) = 0.1489 pi(T) = 0.3253 Rate matrix Q: A -0.8606 0.1874 0.2762 0.3971 C 0.4543 -1.239 0.1818 0.6033 G 0.6902 0.1874 -1.275 0.3971 T 0.4543 0.2847 0.1818 -0.9207 Model of rate heterogeneity: Gamma with 4 categories Gamma shape alpha: 0.551 Category Relative_rate Proportion 1 0.04318 0.25 2 0.2839 0.25 3 0.8541 0.25 4 2.819 0.25 Relative rates are computed as MEAN of the portion of the Gamma distribution falling in the category. MAXIMUM LIKELIHOOD TREE ----------------------- Log-likelihood of the tree: -4555.7776 (s.e. 87.9063) Unconstrained log-likelihood (without tree): -4137.8401 Number of free parameters (#branches + #model parameters): 14 Akaike information criterion (AIC) score: 9139.5551 Corrected Akaike information criterion (AICc) score: 9139.9982 Bayesian information criterion (BIC) score: 9207.7359 Total tree length (sum of branch lengths): 1.5812 Sum of internal branch lengths: 0.2811 (17.7808% of tree length) NOTE: Tree is UNROOTED although outgroup taxon 'Derbesia_sp_WEST4838' is drawn at root Numbers in parentheses are ultrafast bootstrap support (%) +-------------------------------Derbesia_sp_WEST4838 | | +-----------------------------Caulerpa_cliftonii_HV03798 | +-----------------| (100) | | | +----------------Chlorodesmis_fastigiata_HV03865 | | +--| (63) | | +--------Flabellia_petiolata_HV01202 +----------| (81) | +---------------------------------Avrainvillea_mazei_HV02664 | +---------------------Bryopsis_plumosa_WEST4718 Tree in newick format: (Derbesia_sp_WEST4838:0.2868132891,((Caulerpa_cliftonii_HV03798:0.2728587814,(Chlorodesmis_fastigiata_HV03865:0.1539886901,Flabellia_petiolata_HV01202:0.0808826246)63:0.0223449731)100:0.1607568210,Avrainvillea_mazei_HV02664:0.3080387093)81:0.0980408932,Bryopsis_plumosa_WEST4718:0.1974356044); CONSENSUS TREE -------------- Consensus tree is constructed from 1000 bootstrap trees Log-likelihood of consensus tree: -4555.777559 Robinson-Foulds distance between ML tree and consensus tree: 0 Branches with support >0.000000% are kept (extended consensus) Branch lengths are optimized by maximum likelihood on original alignment Numbers in parentheses are bootstrap supports (%) +-------------------------------Derbesia_sp_WEST4838 | | +-----------------------------Caulerpa_cliftonii_HV03798 | +-----------------| (100) | | | +----------------Chlorodesmis_fastigiata_HV03865 | | +--| (63) | | +--------Flabellia_petiolata_HV01202 +----------| (81) | +---------------------------------Avrainvillea_mazei_HV02664 | +---------------------Bryopsis_plumosa_WEST4718 Consensus tree in newick format: (Derbesia_sp_WEST4838:0.2868207186,((Caulerpa_cliftonii_HV03798:0.2729562990,(Chlorodesmis_fastigiata_HV03865:0.1540181569,Flabellia_petiolata_HV01202:0.0809055224)63:0.0222753277)100:0.1607877490,Avrainvillea_mazei_HV02664:0.3080731097)81:0.0980499278,Bryopsis_plumosa_WEST4718:0.1974507790); TIME STAMP ---------- Date and time: Sat Dec 16 03:42:29 2023 Total CPU time used: 1.277007 seconds (0h:0m:1s) Total wall-clock time used: 1.907408528 seconds (0h:0m:1s)
IQ-TREE multicore version 2.2.0.3 COVID-edition for Linux 64-bit built Aug 2 2022
Developed by Bui Quang Minh, James Barbetti, Nguyen Lam Tung,
Olga Chernomor, Heiko Schmidt, Dominik Schrempf, Michael Woodhams, Ly Trong Nhan.
Host: herbairumphylo (AVX512, FMA3, 283 GB RAM)
Command: iqtree2 -s results/alignment/trimmed_cds/OG0000000.trimmed.cds.alignment.fa -bb 1000 -m TEST -nt 1 -mset mrbayes -pre results/gene_tree/OG0000000/OG0000000.cds -redo
Seed: 255357 (Using SPRNG - Scalable Parallel Random Number Generator)
Time: Sat Dec 16 03:42:27 2023
Kernel: AVX+FMA - 1 threads (32 CPU cores detected)
HINT: Use -nt option to specify number of threads because your CPU has 32 cores!
HINT: -nt AUTO will automatically determine the best number of threads to use.
Reading alignment file results/alignment/trimmed_cds/OG0000000.trimmed.cds.alignment.fa ... Fasta format detected
Reading fasta file: done in 0.000155047 secs
Alignment most likely contains DNA/RNA sequences
Constructing alignment: done in 0.000965245 secs
Alignment has 6 sequences with 963 columns, 334 distinct patterns
249 parsimony-informative, 259 singleton sites, 455 constant sites
Gap/Ambiguity Composition p-value
Analyzing sequences: done in 1.68681e-05 secs
1 Derbesia_sp_WEST4838 1.56% passed 91.88%
2 Caulerpa_cliftonii_HV03798 0.00% passed 98.01%
3 Avrainvillea_mazei_HV02664 2.80% passed 18.77%
4 Chlorodesmis_fastigiata_HV03865 3.74% passed 85.62%
5 Flabellia_petiolata_HV01202 5.92% passed 93.93%
6 Bryopsis_plumosa_WEST4718 0.93% passed 76.72%
**** TOTAL 2.49% 0 sequences failed composition chi2 test (p-value<5%; df=3)
Checking for duplicate sequences: done in 2.63005e-05 secs
Create initial parsimony tree by phylogenetic likelihood library (PLL)... 0.011 seconds
Perform fast likelihood tree search using GTR+I+G model...
Estimate model parameters (epsilon = 5.000)
Perform nearest neighbor interchange...
Optimizing NNI: done in 0.00157104 secs using 57.03% CPU
Estimate model parameters (epsilon = 1.000)
1. Initial log-likelihood: -4544.868
Optimal log-likelihood: -4544.854
Rate parameters: A-C: 2.70521 A-G: 3.27681 A-T: 2.57568 C-G: 3.15656 C-T: 3.89217 G-T: 1.00000
Base frequencies: A: 0.372 C: 0.154 G: 0.149 T: 0.325
Proportion of invariable sites: 0.241
Gamma shape alpha: 1.205
Parameters optimization took 1 rounds (0.004 sec)
Time for fast ML tree search: 0.030 seconds
NOTE: ModelFinder requires 1 MB RAM!
ModelFinder will test up to 24 DNA models (sample size: 963) ...
No. Model -LnL df AIC AICc BIC
1 GTR+F 4657.034 17 9348.067 9348.715 9430.858
2 GTR+F+I 4548.126 18 9132.253 9132.977 9219.914
3 GTR+F+G4 4546.645 18 9129.290 9130.015 9216.951
4 GTR+F+I+G4 4544.825 19 9127.650 9128.456 9220.181
6 SYM+I 4671.878 15 9373.757 9374.264 9446.808
7 SYM+G4 4672.933 15 9375.865 9376.372 9448.916
8 SYM+I+G4 4670.387 16 9372.775 9373.350 9450.696
10 HKY+F+I 4557.943 14 9143.885 9144.328 9212.066
11 HKY+F+G4 4555.778 14 9139.556 9139.999 9207.737
12 HKY+F+I+G4 4554.307 15 9138.614 9139.121 9211.665
14 K2P+I 4729.392 11 9480.784 9481.062 9534.355
15 K2P+G4 4732.683 11 9487.367 9487.644 9540.937
16 K2P+I+G4 4729.987 12 9483.975 9484.303 9542.415
18 F81+F+I 4564.150 13 9154.300 9154.683 9217.610
19 F81+F+G4 4563.103 13 9152.205 9152.589 9215.516
20 F81+F+I+G4 4561.524 14 9151.049 9151.492 9219.229
22 JC+I 4729.397 10 9478.793 9479.024 9527.494
23 JC+G4 4732.692 10 9485.384 9485.615 9534.084
24 JC+I+G4 4730.011 11 9482.022 9482.300 9535.593
Akaike Information Criterion: GTR+F+I+G4
Corrected Akaike Information Criterion: GTR+F+I+G4
Bayesian Information Criterion: HKY+F+G4
Best-fit model: HKY+F+G4 chosen according to BIC
All model information printed to results/gene_tree/OG0000000/OG0000000.cds.model.gz
CPU time for ModelFinder: 0.145 seconds (0h:0m:0s)
Wall-clock time for ModelFinder: 0.340 seconds (0h:0m:0s)
Generating 1000 samples for ultrafast bootstrap (seed: 255357)...
NOTE: 1 MB RAM (0 GB) is required!
Estimate model parameters (epsilon = 0.100)
1. Initial log-likelihood: -4555.778
Optimal log-likelihood: -4555.778
Rate parameters: A-C: 1.00000 A-G: 1.51915 A-T: 1.00000 C-G: 1.00000 C-T: 1.51915 G-T: 1.00000
Base frequencies: A: 0.372 C: 0.154 G: 0.149 T: 0.325
Gamma shape alpha: 0.552
Parameters optimization took 1 rounds (0.002 sec)
Wrote distance file to...
Computing ML distances based on estimated model parameters...
Calculating distance matrix: done in 0.000212327 secs using 88.07% CPU
Computing ML distances took 0.000285 sec (of wall-clock time) 0.000238 sec (of CPU time)
Setting up auxiliary I and S matrices: done in 5.37783e-05 secs using 87.4% CPU
Constructing RapidNJ tree: done in 4.2364e-05 secs using 87.34% CPU
Computing RapidNJ tree took 0.000176 sec (of wall-clock time) 0.000154 sec (of CPU time)
Log-likelihood of RapidNJ tree: -4555.778
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| INITIALIZING CANDIDATE TREE SET |
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Generating 99 parsimony trees... 0.052 second
Computing log-likelihood of 6 initial trees ... 0.004 seconds
Current best score: -4555.778
Do NNI search on 7 best initial trees
Optimizing NNI: done in 0.00235233 secs using 99.86% CPU
Optimizing NNI: done in 0.00452666 secs using 99.94% CPU
Optimizing NNI: done in 0.00456644 secs using 98.68% CPU
Optimizing NNI: done in 0.00689326 secs using 98.63% CPU
Optimizing NNI: done in 0.0152205 secs using 45.99% CPU
Optimizing NNI: done in 0.00445433 secs using 99.95% CPU
Optimizing NNI: done in 0.0045559 secs using 99.94% CPU
Finish initializing candidate tree set (7)
Current best tree score: -4555.778 / CPU time: 0.146
Number of iterations: 7
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| OPTIMIZING CANDIDATE TREE SET |
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Optimizing NNI: done in 0.00873475 secs using 77.23% CPU
Optimizing NNI: done in 0.00414177 secs using 99.93% CPU
Optimizing NNI: done in 0.00649399 secs using 99.95% CPU
Iteration 10 / LogL: -4555.817 / Time: 0h:0m:0s
Optimizing NNI: done in 0.0224988 secs using 28.85% CPU
Optimizing NNI: done in 0.00653482 secs using 99.96% CPU
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Optimizing NNI: done in 0.0223075 secs using 28.31% CPU
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Optimizing NNI: done in 0.00654641 secs using 99.96% CPU
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Optimizing NNI: done in 0.00401352 secs using 99.91% CPU
Optimizing NNI: done in 0.00417101 secs using 97.99% CPU
Optimizing NNI: done in 0.00407655 secs using 99.91% CPU
Iteration 20 / LogL: -4555.779 / Time: 0h:0m:0s
Optimizing NNI: done in 0.00651368 secs using 99.96% CPU
Optimizing NNI: done in 0.0131022 secs using 31.99% CPU
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Optimizing NNI: done in 0.00405721 secs using 99.92% CPU
Optimizing NNI: done in 0.02802 secs using 14.39% CPU
UPDATE BEST LOG-LIKELIHOOD: -4555.778
Optimizing NNI: done in 0.00682958 secs using 97.52% CPU
Optimizing NNI: done in 0.00422876 secs using 99.91% CPU
UPDATE BEST LOG-LIKELIHOOD: -4555.778
Optimizing NNI: done in 0.0224705 secs using 28.75% CPU
Optimizing NNI: done in 0.00415488 secs using 99.93% CPU
Iteration 30 / LogL: -4555.790 / Time: 0h:0m:0s (0h:0m:1s left)
Optimizing NNI: done in 0.00411438 secs using 99.94% CPU
UPDATE BEST LOG-LIKELIHOOD: -4555.778
Optimizing NNI: done in 0.0039807 secs using 99.93% CPU
UPDATE BEST LOG-LIKELIHOOD: -4555.778
Optimizing NNI: done in 0.00638156 secs using 99.96% CPU
Optimizing NNI: done in 0.00654908 secs using 99.94% CPU
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Optimizing NNI: done in 0.00619934 secs using 99.95% CPU
Optimizing NNI: done in 0.0200564 secs using 20.23% CPU
Iteration 40 / LogL: -4555.856 / Time: 0h:0m:0s (0h:0m:1s left)
Optimizing NNI: done in 0.00630544 secs using 99.96% CPU
Optimizing NNI: done in 0.00630767 secs using 99.94% CPU
Optimizing NNI: done in 0.0128042 secs using 48.94% CPU
Optimizing NNI: done in 0.00437976 secs using 94.64% CPU
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Optimizing NNI: done in 0.0201936 secs using 20.76% CPU
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Optimizing NNI: done in 0.00418168 secs using 99.89% CPU
Iteration 50 / LogL: -4555.788 / Time: 0h:0m:1s (0h:0m:1s left)
Log-likelihood cutoff on original alignment: -4567.116
Optimizing NNI: done in 0.00433666 secs using 97.1% CPU
Optimizing NNI: done in 0.00775192 secs using 99.95% CPU
Optimizing NNI: done in 0.00465842 secs using 99.93% CPU
Optimizing NNI: done in 0.00526458 secs using 93.95% CPU
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Optimizing NNI: done in 0.00501295 secs using 99.9% CPU
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Optimizing NNI: done in 0.00788034 secs using 47.69% CPU
Iteration 60 / LogL: -4555.781 / Time: 0h:0m:1s (0h:0m:0s left)
Optimizing NNI: done in 0.00474414 secs using 99.93% CPU
Optimizing NNI: done in 0.00736919 secs using 99.97% CPU
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Optimizing NNI: done in 0.00477421 secs using 99.95% CPU
Iteration 70 / LogL: -4555.789 / Time: 0h:0m:1s (0h:0m:0s left)
Optimizing NNI: done in 0.00721657 secs using 99.95% CPU
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Iteration 80 / LogL: -4555.780 / Time: 0h:0m:1s (0h:0m:0s left)
Optimizing NNI: done in 0.00404481 secs using 99.86% CPU
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Optimizing NNI: done in 0.00433678 secs using 93.8% CPU
Iteration 90 / LogL: -4555.821 / Time: 0h:0m:1s (0h:0m:0s left)
Optimizing NNI: done in 0.00661973 secs using 95.47% CPU
Optimizing NNI: done in 0.00660723 secs using 95.64% CPU
Optimizing NNI: done in 0.00650325 secs using 39.53% CPU
Optimizing NNI: done in 0.00449954 secs using 90.76% CPU
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Optimizing NNI: done in 0.00441981 secs using 93.94% CPU
Optimizing NNI: done in 0.00659543 secs using 37.24% CPU
Optimizing NNI: done in 0.00654642 secs using 95.53% CPU
Optimizing NNI: done in 0.00433021 secs using 93.58% CPU
Iteration 100 / LogL: -4555.821 / Time: 0h:0m:1s (0h:0m:0s left)
Log-likelihood cutoff on original alignment: -4567.116
NOTE: Bootstrap correlation coefficient of split occurrence frequencies: 1.000
Optimizing NNI: done in 0.00652269 secs using 97.08% CPU
TREE SEARCH COMPLETED AFTER 101 ITERATIONS / Time: 0h:0m:1s
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| FINALIZING TREE SEARCH |
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Performs final model parameters optimization
Estimate model parameters (epsilon = 0.010)
1. Initial log-likelihood: -4555.778
Optimal log-likelihood: -4555.778
Rate parameters: A-C: 1.00000 A-G: 1.51939 A-T: 1.00000 C-G: 1.00000 C-T: 1.51939 G-T: 1.00000
Base frequencies: A: 0.372 C: 0.154 G: 0.149 T: 0.325
Gamma shape alpha: 0.551
Parameters optimization took 1 rounds (0.003 sec)
BEST SCORE FOUND : -4555.778
Creating bootstrap support values...
Split supports printed to NEXUS file results/gene_tree/OG0000000/OG0000000.cds.splits.nex
Total tree length: 1.581
Total number of iterations: 101
CPU time used for tree search: 1.222 sec (0h:0m:1s)
Wall-clock time used for tree search: 1.801 sec (0h:0m:1s)
Total CPU time used: 1.277 sec (0h:0m:1s)
Total wall-clock time used: 1.898 sec (0h:0m:1s)
Computing bootstrap consensus tree...
Reading input file results/gene_tree/OG0000000/OG0000000.cds.splits.nex...
6 taxa and 12 splits.
Consensus tree written to results/gene_tree/OG0000000/OG0000000.cds.contree
Reading input trees file results/gene_tree/OG0000000/OG0000000.cds.contree
Log-likelihood of consensus tree: -4555.778
Analysis results written to:
IQ-TREE report: results/gene_tree/OG0000000/OG0000000.cds.iqtree
Maximum-likelihood tree: results/gene_tree/OG0000000/OG0000000.cds.treefile
Likelihood distances: results/gene_tree/OG0000000/OG0000000.cds.mldist
Ultrafast bootstrap approximation results written to:
Split support values: results/gene_tree/OG0000000/OG0000000.cds.splits.nex
Consensus tree: results/gene_tree/OG0000000/OG0000000.cds.contree
Screen log file: results/gene_tree/OG0000000/OG0000000.cds.log
ALISIM COMMAND
--------------
--alisim simulated_MSA -t results/gene_tree/OG0000000/OG0000000.cds.treefile -m "HKY{1.51939}+F{0.372204,0.153532,0.148917,0.325346}+G4{0.550981}" --length 963
Date and Time: Sat Dec 16 03:42:29 2023
Supertree
Workflow
Bibliography
- 1
- Deren A. R. Eaton. Toytree: A minimalist tree visualization and manipulation library for Python. Methods in Ecology and Evolution, 11:187–191, 2020. doi:10.1111/2041-210X.13313.
- 2
- David M. Emms and Steven Kelly. Orthofinder: phylogenetic orthology inference for comparative genomics. Genome Biology, 20(1):238, 2019. URL: https://doi.org/10.1186/s13059-019-1832-y, doi:10.1186/s13059-019-1832-y.
- 3
- Diep Thi Hoang, Olga Chernomor, Arndt von Haeseler, Bui Quang Minh, and Le Sy Vinh. UFBoot2: Improving the Ultrafast Bootstrap Approximation. Molecular Biology and Evolution, 35(2):518–522, 10 2017. URL: https://doi.org/10.1093/molbev/msx281, arXiv:https://academic.oup.com/mbe/article-pdf/35/2/518/24367824/msx281.pdf, doi:10.1093/molbev/msx281.
- 4
- Subha Kalyaanamoorthy, Bui Quang Minh, Thomas K F Wong, Arndt von Haeseler, and Lars S Jermiin. Modelfinder: fast model selection for accurate phylogenetic estimates. Nature Methods, 14(6):587–589, 2017. URL: https://doi.org/10.1038/nmeth.4285, doi:10.1038/nmeth.4285.
- 5
- Kazutaka Katoh and Daron M. Standley. MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability. Molecular Biology and Evolution, 30(4):772–780, 01 2013. URL: https://doi.org/10.1093/molbev/mst010, arXiv:https://academic.oup.com/mbe/article-pdf/30/4/772/6420419/mst010.pdf, doi:10.1093/molbev/mst010.
- 6
- Bui Quang Minh, Heiko A Schmidt, Olga Chernomor, Dominik Schrempf, Michael D Woodhams, Arndt von Haeseler, and Robert Lanfear. IQ-TREE 2: New Models and Efficient Methods for Phylogenetic Inference in the Genomic Era. Molecular Biology and Evolution, 37(5):1530–1534, 02 2020. URL: https://doi.org/10.1093/molbev/msaa015, arXiv:https://academic.oup.com/mbe/article-pdf/37/5/1530/33386032/msaa015.pdf, doi:10.1093/molbev/msaa015.
- 7
- Jacob L Steenwyk, III Buida, Thomas J, Abigail L Labella, Yuanning Li, Xing-Xing Shen, and Antonis Rokas. PhyKIT: a broadly applicable UNIX shell toolkit for processing and analyzing phylogenomic data. Bioinformatics, 37(16):2325–2331, 02 2021. URL: https://doi.org/10.1093/bioinformatics/btab096, arXiv:https://academic.oup.com/bioinformatics/article-pdf/37/16/2325/39948152/btab096.pdf, doi:10.1093/bioinformatics/btab096.
- 8
- Jacob L. Steenwyk, Thomas J. Buida, Carla Gonçalves, Dayna C. Goltz, Grace Morales, Matthew E. Mead, Abigail L. LaBella, Christina M. Chavez, Jonathan E. Schmitz, Maria Hadjifrangiskou, Yuanning Li, and Antonis Rokas. BioKIT: a versatile toolkit for processing and analyzing diverse types of sequence data. biorxiv, oct 2021. URL: https://doi.org/10.1101%2F2021.10.02.462868, doi:10.1101/2021.10.02.462868.
- 9
- Jacob L. Steenwyk, Thomas J. Buida, III, Yuanning Li, Xing-Xing Shen, and Antonis Rokas. Clipkit: a multiple sequence alignment trimming software for accurate phylogenomic inference. PLOS Biology, 18(12):1–17, 12 2020. URL: https://doi.org/10.1371/journal.pbio.3001007, doi:10.1371/journal.pbio.3001007.
- 10
- Chao Zhang, Maryam Rabiee, Erfan Sayyari, and Siavash Mirarab. Astral-iii: polynomial time species tree reconstruction from partially resolved gene trees. BMC Bioinformatics, 19(6):153, 2018. URL: https://doi.org/10.1186/s12859-018-2129-y, doi:10.1186/s12859-018-2129-y.
@article{10.1093/molbev/mst010,
author = "Katoh, Kazutaka and Standley, Daron M.",
title = "{MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability}",
journal = "Molecular Biology and Evolution",
volume = "30",
number = "4",
pages = "772-780",
year = "2013",
month = "01",
abstract = "{We report a major update of the MAFFT multiple sequence alignment program. This version has several new features, including options for adding unaligned sequences into an existing alignment, adjustment of direction in nucleotide alignment, constrained alignment and parallel processing, which were implemented after the previous major update. This report shows actual examples to explain how these features work, alone and in combination. Some examples incorrectly aligned by MAFFT are also shown to clarify its limitations. We discuss how to avoid misalignments, and our ongoing efforts to overcome such limitations.}",
issn = "0737-4038",
doi = "10.1093/molbev/mst010",
url = "https://doi.org/10.1093/molbev/mst010",
eprint = "https://academic.oup.com/mbe/article-pdf/30/4/772/6420419/mst010.pdf"
}
@article{Emms2019,
author = "Emms, David M. and Kelly, Steven",
type = "Journal Article",
title = "OrthoFinder: phylogenetic orthology inference for comparative genomics",
journal = "Genome Biology",
number = "1",
doi = "10.1186/s13059-019-1832-y",
volume = "20",
pages = "238",
url = "https://doi.org/10.1186/s13059-019-1832-y",
year = "2019",
abstract = "Here, we present a major advance of the OrthoFinder method. This extends OrthoFinder’s high accuracy orthogroup inference to provide phylogenetic inference of orthologs, rooted gene trees, gene duplication events, the rooted species tree, and comparative genomics statistics. Each output is benchmarked on appropriate real or simulated datasets, and where comparable methods exist, OrthoFinder is equivalent to or outperforms these methods. Furthermore, OrthoFinder is the most accurate ortholog inference method on the Quest for Orthologs benchmark test. Finally, OrthoFinder’s comprehensive phylogenetic analysis is achieved with equivalent speed and scalability to the fastest, score-based heuristic methods. OrthoFinder is available at https://github.com/davidemms/OrthoFinder.",
isbn = "1474-760X",
DA = "2019/11/14"
}
@article{10.1371/journal.pbio.3001007,
author = "Steenwyk, Jacob L. and Buida, III, Thomas J. and Li, Yuanning and Shen, Xing-Xing and Rokas, Antonis",
doi = "10.1371/journal.pbio.3001007",
journal = "PLOS Biology",
publisher = "Public Library of Science",
title = "ClipKIT: A multiple sequence alignment trimming software for accurate phylogenomic inference",
year = "2020",
month = "12",
volume = "18",
url = "https://doi.org/10.1371/journal.pbio.3001007",
pages = "1-17",
abstract = "Highly divergent sites in multiple sequence alignments (MSAs), which can stem from erroneous inference of homology and saturation of substitutions, are thought to negatively impact phylogenetic inference. Thus, several different trimming strategies have been developed for identifying and removing these sites prior to phylogenetic inference. However, a recent study reported that doing so can worsen inference, underscoring the need for alternative alignment trimming strategies. Here, we introduce ClipKIT, an alignment trimming software that, rather than identifying and removing putatively phylogenetically uninformative sites, instead aims to identify and retain parsimony-informative sites, which are known to be phylogenetically informative. To test the efficacy of ClipKIT, we examined the accuracy and support of phylogenies inferred from 14 different alignment trimming strategies, including those implemented in ClipKIT, across nearly 140,000 alignments from a broad sampling of evolutionary histories. Phylogenies inferred from ClipKIT-trimmed alignments are accurate, robust, and time saving. Furthermore, ClipKIT consistently outperformed other trimming methods across diverse datasets, suggesting that strategies based on identifying and retaining parsimony-informative sites provide a robust framework for alignment trimming.",
number = "12"
}
@article{Steenwyk_2021,
author = "Steenwyk, Jacob L. and Buida, Thomas J. and Gon{\c{c}}alves, Carla and Goltz, Dayna C. and Morales, Grace and Mead, Matthew E. and LaBella, Abigail L. and Chavez, Christina M. and Schmitz, Jonathan E. and Hadjifrangiskou, Maria and Li, Yuanning and Rokas, Antonis",
doi = "10.1101/2021.10.02.462868",
url = "https://doi.org/10.1101\%2F2021.10.02.462868",
year = "2021",
month = "oct",
journal = "biorxiv",
publisher = "Cold Spring Harbor Laboratory",
title = "{BioKIT}: a versatile toolkit for processing and analyzing diverse types of sequence data"
}
@article{10.1093/molbev/msx281,
author = "Hoang, Diep Thi and Chernomor, Olga and von Haeseler, Arndt and Minh, Bui Quang and Vinh, Le Sy",
title = "{UFBoot2: Improving the Ultrafast Bootstrap Approximation}",
journal = "Molecular Biology and Evolution",
volume = "35",
number = "2",
pages = "518-522",
year = "2017",
month = "10",
abstract = "{The standard bootstrap (SBS), despite being computationally intensive, is widely used in maximum likelihood phylogenetic analyses. We recently proposed the ultrafast bootstrap approximation (UFBoot) to reduce computing time while achieving more unbiased branch supports than SBS under mild model violations. UFBoot has been steadily adopted as an efficient alternative to SBS and other bootstrap approaches. Here, we present UFBoot2, which substantially accelerates UFBoot and reduces the risk of overestimating branch supports due to polytomies or severe model violations. Additionally, UFBoot2 provides suitable bootstrap resampling strategies for phylogenomic data. UFBoot2 is 778 times (median) faster than SBS and 8.4 times (median) faster than RAxML rapid bootstrap on tested data sets. UFBoot2 is implemented in the IQ-TREE software package version 1.6 and freely available at http://www.iqtree.org.}",
issn = "0737-4038",
doi = "10.1093/molbev/msx281",
url = "https://doi.org/10.1093/molbev/msx281",
eprint = "https://academic.oup.com/mbe/article-pdf/35/2/518/24367824/msx281.pdf"
}
@article{10.1093/bioinformatics/btab096,
author = "Steenwyk, Jacob L and Buida, Thomas J, III and Labella, Abigail L and Li, Yuanning and Shen, Xing-Xing and Rokas, Antonis",
title = "{PhyKIT: a broadly applicable UNIX shell toolkit for processing and analyzing phylogenomic data}",
journal = "Bioinformatics",
volume = "37",
number = "16",
pages = "2325-2331",
year = "2021",
month = "02",
abstract = "{Diverse disciplines in biology process and analyze multiple sequence alignments (MSAs) and phylogenetic trees to evaluate their information content, infer evolutionary events and processes and predict gene function. However, automated processing of MSAs and trees remains a challenge due to the lack of a unified toolkit. To fill this gap, we introduce PhyKIT, a toolkit for the UNIX shell environment with 30 functions that process MSAs and trees, including but not limited to estimation of mutation rate, evaluation of sequence composition biases, calculation of the degree of violation of a molecular clock and collapsing bipartitions (internal branches) with low support.To demonstrate the utility of PhyKIT, we detail three use cases: (1) summarizing information content in MSAs and phylogenetic trees for diagnosing potential biases in sequence or tree data; (2) evaluating gene–gene covariation of evolutionary rates to identify functional relationships, including novel ones, among genes and (3) identify lack of resolution events or polytomies in phylogenetic trees, which are suggestive of rapid radiation events or lack of data. We anticipate PhyKIT will be useful for processing, examining and deriving biological meaning from increasingly large phylogenomic datasets.PhyKIT is freely available on GitHub (https://github.com/JLSteenwyk/PhyKIT), PyPi (https://pypi.org/project/phykit/) and the Anaconda Cloud (https://anaconda.org/JLSteenwyk/phykit) under the MIT license with extensive documentation and user tutorials (https://jlsteenwyk.com/PhyKIT).Supplementary data are available at Bioinformatics online.}",
issn = "1367-4803",
doi = "10.1093/bioinformatics/btab096",
url = "https://doi.org/10.1093/bioinformatics/btab096",
eprint = "https://academic.oup.com/bioinformatics/article-pdf/37/16/2325/39948152/btab096.pdf"
}
@article{eaton_toytree_2020,
author = "Eaton, Deren A. R.",
title = "Toytree: {A} minimalist tree visualization and manipulation library for {Python}",
volume = "11",
doi = "10.1111/2041-210X.13313",
journal = "Methods in Ecology and Evolution",
year = "2020",
pages = "187--191"
}
@article{10.1093/molbev/msaa015,
author = "Minh, Bui Quang and Schmidt, Heiko A and Chernomor, Olga and Schrempf, Dominik and Woodhams, Michael D and von Haeseler, Arndt and Lanfear, Robert",
title = "{IQ-TREE 2: New Models and Efficient Methods for Phylogenetic Inference in the Genomic Era}",
journal = "Molecular Biology and Evolution",
volume = "37",
number = "5",
pages = "1530-1534",
year = "2020",
month = "02",
abstract = "{IQ-TREE (http://www.iqtree.org, last accessed February 6, 2020) is a user-friendly and widely used software package for phylogenetic inference using maximum likelihood. Since the release of version 1 in 2014, we have continuously expanded IQ-TREE to integrate a plethora of new models of sequence evolution and efficient computational approaches of phylogenetic inference to deal with genomic data. Here, we describe notable features of IQ-TREE version 2 and highlight the key advantages over other software.}",
issn = "0737-4038",
doi = "10.1093/molbev/msaa015",
url = "https://doi.org/10.1093/molbev/msaa015",
eprint = "https://academic.oup.com/mbe/article-pdf/37/5/1530/33386032/msaa015.pdf"
}
@article{Kalyaanamoorthy2017,
author = "Kalyaanamoorthy, Subha and Minh, Bui Quang and Wong, Thomas K F and von Haeseler, Arndt and Jermiin, Lars S",
type = "Journal Article",
title = "ModelFinder: fast model selection for accurate phylogenetic estimates",
journal = "Nature Methods",
number = "6",
doi = "10.1038/nmeth.4285",
volume = "14",
pages = "587--589",
url = "https://doi.org/10.1038/nmeth.4285",
year = "2017",
abstract = "ModelFinder is a fast model-selection method that greatly improves the accuracy of phylogenetic estimates.",
issn = "1548-7105",
DA = "2017/06/01"
}
@article{Zhang2018,
author = "Zhang, Chao and Rabiee, Maryam and Sayyari, Erfan and Mirarab, Siavash",
type = "Journal Article",
title = "ASTRAL-III: polynomial time species tree reconstruction from partially resolved gene trees",
journal = "BMC Bioinformatics",
number = "6",
doi = "10.1186/s12859-018-2129-y",
volume = "19",
pages = "153",
url = "https://doi.org/10.1186/s12859-018-2129-y",
year = "2018",
abstract = "Evolutionary histories can be discordant across the genome, and such discordances need to be considered in reconstructing the species phylogeny. ASTRAL is one of the leading methods for inferring species trees from gene trees while accounting for gene tree discordance. ASTRAL uses dynamic programming to search for the tree that shares the maximum number of quartet topologies with input gene trees, restricting itself to a predefined set of bipartitions.",
issn = "1471-2105",
DA = "2018/05/08"
}
File(s) not Fasta or Genbank file. Suffix from file 'NC_026795-truncated.txt' is not Fasta or Genbank. File is assumed to be in Fasta format.